Corpus Engine Towards a reproducible .science file.
← All .science files

pmid:40797087

Dehydrotanshinone II A alleviates osteoarthritis via activating PPARγ to inhibit ferroptosis in chondrocytes.

Wenli Guan · Fahu Yuan · Xin Wang

Scientific reports · 2025 doi:10.1038/s41598-025-14896-y

Paper

complete

Experiment

complete

Data

partial

Analysis

complete

Execution

absent

Execution evidence has not yet been added to this .science file. Explore its methods, data and open questions to plan the next step.
Record details sci_version · id · kind · revision · content_hash · schema · created_at · updated_at · generator
id
pmid:40797087
kind
science-record
content_hash
sha256:0255801004f6e247522ee06fa81956364844871c1223553d98a522e95c9f4eee
schema
https://corpus.bntrg.co.uk/sci/1.0/sci.schema.json
created_at
2026-11-01T20:30:53Z
updated_at
2026-11-01T22:57:00Z
generator object · 2 fields
name
corpus-assay-engine
run_id
reading-sci-2026-11-01
paper object · 10 fields
state
complete
title
Dehydrotanshinone II A alleviates osteoarthritis via activating PPARγ to inhibit ferroptosis in chondrocytes.
doi
10.1038/s41598-025-14896-y
pmid
40797087
authors array · 3 items
[0]
Wenli Guan
[1]
Fahu Yuan
[2]
Xin Wang
journal
Scientific reports
year
2025
abstract
Osteoarthritis (OA) is a prevalent chronic degenerative joint disease. Ferroptosis, an iron-dependent form of programmed cell death, has been implicated as a crucial contributor to OA progression. Simiao Powder, a classical traditional Chinese medicine formula, has been widely used in clinical practice to treat inflammatory diseases such as gout and OA. However, its regulatory effects on ferroptosis remain unclear. This study investigates whether Simiao Powder could alleviate OA by regulating ferroptosis and analyzes its underlying mechanisms. We integrated multiple bioinformatics analyses along with in vivo and in vitro experiments to elucidate the mechanism by which DHT IIA treats OA. Potential therapeutic targets of Simiao Powder were identified through the TCMSP and GEO databases, and their potential biological functions were evaluated using GO enrichment, ROC curve analysis, molecular docking, and immune infiltration assessment via CIBERSORTx. OA was induced in SD rats using a high carbohydrate and fat diet, followed by a 16-week intervention with DHT IIA. Histological staining, OARSI scoring, and cartilage thickness measurements were performed. The expression levels of PPARγ, GPX4, and the apoptosis marker TUNEL in rat cartilage were evaluated using immunofluorescence and immunohistochemistry. In an LPS-induced ATDC5 chondrocyte injury model, Western blotting was used to assess the expression of PPARγ, COL2A1, ACSL4, and MMP13. Furthermore, the scTenifoldKnk algorithm was applied to perform a virtual knockout of PPARγ based on the GSE216651 single-cell RNA-seq dataset to explore its downstream regulatory effects. Bioinformatics analysis identified five key genes (CDKN1A, HMOX1, DPP4, GJA1, and PPARγ), among which PPARγ and HMOX1 exhibited strong predictive potential with AUC values > 0.8. Molecular docking analysis revealed that DHT IIA exhibited the lowest binding energy with PPARγ (-8.15 kcal/mol), indicating it as the most likely therapeutic target. In vitro and in vivo experiments demonstrated that DHT IIA significantly upregulated PPARγ expression reduced ACSL4, MMP13 and TUNEL levels, increased COL2A1 and GPX4 expression levels. Meanwhile computer simulated gene knockdown also laterally confirmed that PPARγ is a key gene affecting ferroptosis and OA development. The study confirmed that DHT IIA could improve the articular cartilage structure of OA rats by elevating PPARγ and inhibiting ferroptosis. This study reveals that DHT IIA, the active ingredient of Simiao Powder, may alleviate OA by inhibiting ferroptosis through the activation of PPARγ. These findings provide a new molecular mechanism basis for the treatment of OA by Simiao Powder, as well as scientific support for the subsequent drug development and clinical applications.
claims array · 3 items
[0] object · 6 fields
id
claim-method
statement
For data that met the normal distribution and variance chi-square, a one-way ANOVA was performed followed by multiple comparisons using Tukey’s post hoc test. For data that did not meet the assumption of normality, the Kruskal-Wallis H test was used. If significant differences were observed (p < 0.05), pairwise comparisons were performed using Dunn’s test with Bonferroni correction.
kind
methodological
target
null
evidence array · 1 item
[0] object · 3 fields
asset
source:pmid:40797087
locator
sections[20] "Statistical analysis" paragraph 2
quote
For data that met the normal distribution and variance chi-square, a one-way ANOVA was performed followed by multiple comparisons using Tukey’s post hoc test. For data that did not meet the assumption of normality, the Kruskal-Wallis H test was used. If significant differences were observed (p < 0.05), pairwise comparisons were performed using Dunn’s test with Bonferroni correction.
state
complete
[1] object · 6 fields
id
claim-data-access
statement
The datasets used in this study are publicly accessible. The datasets included in this study can be downloaded from the GEO database (GSE98918: https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE98918; GSE178557: https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE178557), whose corresponding data are cited in references [18, 19]. Further inquiries can be directed to the corresponding author.
kind
methodological
target
null
evidence array · 1 item
[0] object · 3 fields
asset
source:pmid:40797087
locator
sections[37] "Data availability" paragraph 2
quote
The datasets used in this study are publicly accessible. The datasets included in this study can be downloaded from the GEO database (GSE98918: https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE98918; GSE178557: https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE178557), whose corresponding data are cited in references [18, 19]. Further inquiries can be directed to the corresponding author.
state
complete
[2] object · 6 fields
id
claim-target-result
statement
Bioinformatics analysis identified five key genes (CDKN1A, HMOX1, DPP4, GJA1, and PPARγ), among which PPARγ and HMOX1 exhibited strong predictive potential with AUC values > 0.8.
kind
qualitative
target
null
evidence array · 1 item
[0] object · 3 fields
asset
source:pmid:40797087
locator
sections[0] "Abstract" paragraph 1
quote
Bioinformatics analysis identified five key genes (CDKN1A, HMOX1, DPP4, GJA1, and PPARγ), among which PPARγ and HMOX1 exhibited strong predictive potential with AUC values > 0.8.
state
complete
gaps array · 0 items
experiment object · 8 fields
state
complete
objective
Bioinformatics analysis identified five key genes (CDKN1A, HMOX1, DPP4, GJA1, and PPARγ), among which PPARγ and HMOX1 exhibited strong predictive potential with AUC values > 0.8.
steps array · 3 items
[0] object · 13 fields
id
read_published_estimate
order
1
name
Read the published estimate from the source
kind
other
state
complete
blocked_on
null
description
The claim, method and evidence span published with the source article.
parameters object · 0 fields
inputs array · 1 item
[0]
source:pmid:40797087
outputs array · 1 item
[0]
the published estimate and its evidence
instruments array · 0 items
reagents array · 0 items
[1] object · 13 fields
id
obtain_source_data
order
2
name
Obtain the source data from the named repository
kind
data-preparation
state
complete
blocked_on
null
description
The GEO series accession resolves and its sample accessions are listed. This lane did not download the dataset or read its licence.
parameters object · 0 fields
inputs array · 1 item
[0]
data:geo:GSE178557
outputs array · 1 item
[0]
the source data with its repository provenance
instruments array · 0 items
reagents array · 0 items
[2] object · 13 fields
id
run_analysis
order
3
name
Run the published analysis
kind
analysis
state
complete
blocked_on
null
description
Apply the paper's statistical method to the resolved series and compare the result with the published target.
parameters object · 0 fields
inputs array · 1 item
[0]
data:geo:GSE178557
outputs array · 1 item
[0]
the replicated result and its comparison
instruments array · 0 items
reagents array · 0 items
materials array · 0 items
instruments array · 0 items
reagents array · 0 items
conditions object · 0 fields
gaps array · 0 items
data object · 3 fields
state
partial
assets array · 4 items
[0] object · 15 fields
id
source:pmid:40797087
role
manuscript
format
xml
media_type
application/xml
uri
https://doi.org/10.1038/s41598-025-14896-y
sha256
sha256:29af428334fd4e19f753b005ed5192c9869a2119eea1657810b575378c33774c
bytes
60027
access
open
state
resolved
reader
null
reader_status
reader_required
identifier
10.1038/s41598-025-14896-y
version
null
note
Full article fetched from PMC; the checksum covers the rendered section body, not the original XML bytes.
structure object · 4 fields
pmcid
PMC12343851
source
europe_pmc_fulltext
coverage
whole_body
text_hash_scope
rendered_section_body
[1] object · 15 fields
id
data:geo:GSE178557
role
raw
format
geo-series
media_type
application/vnd.ncbi.geo-series+json
uri
https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE178557
sha256
null
bytes
null
access
open
state
resolved
reader
null
reader_status
reader_required
identifier
GSE178557
version
null
note
The datasets used in this study are publicly accessible. The datasets included in this study can be downloaded from the GEO database (GSE98918: https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE98918; GSE178557: https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE178557), whose corresponding data are cited in references [18, 19]. Further inquiries can be directed to the corresponding author.
structure object · 15 fields
repository
GEO
access_route
GEO accession URL
access_statement_verbatim
The datasets used in this study are publicly accessible. The datasets included in this study can be downloaded from the GEO database (GSE98918: https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE98918; GSE178557: https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE178557), whose corresponding data are cited in references [18, 19]. Further inquiries can be directed to the corresponding author.
access_statement_kind
data_availability_statement
sample_accessions array · 8 items
[0]
GSM5393765
[1]
GSM5393766
[2]
GSM5393767
[3]
GSM5393768
[4]
GSM5393769
[5]
GSM5393770
[6]
GSM5393771
[7]
GSM5393772
sample_count
8
group_sizes
null
group_sizes_basis
null
platform
13497
taxon
Homo sapiens
title
Microarray identifies differentially expressed mRNAs of cartilages between osteoarthritis (OA) patients and control patients
resolution_checked_at
2026-11-01T19:09:46Z
resolution_check
identifier_resolution_only_no_download_no_licence_read
downloaded
false
licence_read
false
[2] object · 15 fields
id
data:geo:GSE216651
role
raw
format
geo-series
media_type
application/vnd.ncbi.geo-series+json
uri
https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE216651
sha256
null
bytes
null
access
open
state
resolved
reader
null
reader_status
reader_required
identifier
GSE216651
version
null
note
The datasets used in this study are publicly accessible. The datasets included in this study can be downloaded from the GEO database (GSE98918: https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE98918; GSE178557: https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE178557), whose corresponding data are cited in references [18, 19]. Further inquiries can be directed to the corresponding author.
structure object · 15 fields
repository
GEO
access_route
GEO accession URL
access_statement_verbatim
The datasets used in this study are publicly accessible. The datasets included in this study can be downloaded from the GEO database (GSE98918: https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE98918; GSE178557: https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE178557), whose corresponding data are cited in references [18, 19]. Further inquiries can be directed to the corresponding author.
access_statement_kind
data_availability_statement
sample_accessions array · 9 items
[0]
GSM6685302
[1]
GSM6685303
[2]
GSM6685304
[3]
GSM6685305
[4]
GSM6685306
[5]
GSM6685307
[6]
GSM6685308
[7]
GSM6685309
[8]
GSM6685310
sample_count
9
group_sizes
null
group_sizes_basis
null
platform
24676
taxon
Homo sapiens
title
Single-cell atlas of human infrapatellar fat pad and synovium unravels mechanisms of osteoarthritis-induced joint pathology
resolution_checked_at
2026-11-01T20:16:08Z
resolution_check
identifier_resolution_only_no_download_no_licence_read
downloaded
false
licence_read
false
[3] object · 15 fields
id
data:geo:GSE98918
role
raw
format
geo-series
media_type
application/vnd.ncbi.geo-series+json
uri
https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE98918
sha256
null
bytes
null
access
open
state
resolved
reader
null
reader_status
reader_required
identifier
GSE98918
version
null
note
The datasets used in this study are publicly accessible. The datasets included in this study can be downloaded from the GEO database (GSE98918: https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE98918; GSE178557: https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE178557), whose corresponding data are cited in references [18, 19]. Further inquiries can be directed to the corresponding author.
structure object · 15 fields
repository
GEO
access_route
GEO accession URL
access_statement_verbatim
The datasets used in this study are publicly accessible. The datasets included in this study can be downloaded from the GEO database (GSE98918: https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE98918; GSE178557: https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE178557), whose corresponding data are cited in references [18, 19]. Further inquiries can be directed to the corresponding author.
access_statement_kind
data_availability_statement
sample_accessions array · 24 items
[0]
GSM2627518
[1]
GSM2627519
[2]
GSM2627520
[3]
GSM2627521
[4]
GSM2627522
[5]
GSM2627523
[6]
GSM2627524
[7]
GSM2627525
[8]
GSM2627526
[9]
GSM2627527
[10]
GSM2627528
[11]
GSM2627529
[12]
GSM2627530
[13]
GSM2627531
[14]
GSM2627532
[15]
GSM2627533
[16]
GSM2627534
[17]
GSM2627535
[18]
GSM2627536
[19]
GSM2627537
[20]
GSM2627538
[21]
GSM2627539
[22]
GSM2627540
[23]
GSM2627541
sample_count
24
group_sizes
null
group_sizes_basis
null
platform
20844
taxon
Homo sapiens
title
The Impact of Osteoarthritis on the Biology of the Meniscus:
resolution_checked_at
2026-11-01T17:30:42Z
resolution_check
identifier_resolution_only_no_download_no_licence_read
downloaded
false
licence_read
false
gaps array · 6 items
[0]
asset:data:geo:GSE178557 not downloaded
[1]
asset:data:geo:GSE178557 licence not read
[2]
asset:data:geo:GSE216651 not downloaded
[3]
asset:data:geo:GSE216651 licence not read
[4]
asset:data:geo:GSE98918 not downloaded
[5]
asset:data:geo:GSE98918 licence not read
analysis object · 4 fields
state
complete
methods array · 4 items
[0] object · 10 fields
id
method-1
family
group_comparison
specific
anova
label
Group comparison
dsl_operations array · 4 items
[0]
group_summary
[1]
welch_t
[2]
bootstrap_mean_difference
[3]
group_comparison_anova
missing_operations array · 0 items
parameters object · 0 fields
data_shapes array · 1 item
[0]
two_or_more_groups_continuous
evidence object · 3 fields
score
1
band
verbatim
quote
For data that met the normal distribution and variance chi-square, a one-way ANOVA was performed followed by multiple comparisons using Tukey’s post hoc test. For data that did not meet the assumption of normality, the Kruskal-Wallis H test was used. If significant differences were observed (p < 0.05), pairwise comparisons were performed using Dunn’s test with Bonferroni correction.
[1] object · 10 fields
id
method-2
family
network_analysis
specific
pathway_enrichment
label
Network / pathway analysis
dsl_operations array · 1 item
[0]
pathway_enrich
missing_operations array · 0 items
parameters object · 0 fields
data_shapes array · 1 item
[0]
edge_list
evidence object · 3 fields
score
0.7
band
medium
quote
GO enrichment
[2] object · 10 fields
id
method-3
family
diagnostic_evaluation
specific
roc
label
Diagnostic test evaluation
dsl_operations array · 6 items
[0]
confusion_counts
[1]
roc_curve
[2]
sensitivity_specificity
[3]
solve_confusion_matrix
[4]
classification_metrics
[5]
published_precision_envelope
missing_operations array · 0 items
parameters object · 0 fields
data_shapes array · 1 item
[0]
reference_standard_and_test
evidence object · 3 fields
score
0.7
band
medium
quote
ROC curve
[3] object · 10 fields
id
method-4
family
contingency_analysis
specific
chi_square
label
Categorical (contingency table) analysis
dsl_operations array · 1 item
[0]
chi_square_test
missing_operations array · 0 items
parameters object · 0 fields
data_shapes array · 1 item
[0]
categorical_cross_tabulation
evidence object · 3 fields
score
0.8
band
high
quote
chi-square
targets array · 0 items
gaps array · 0 items
capability object · 3 fields
state
complete
requirements array · 1 item
[0] object · 6 fields
capability_id
capability:computational_analysis
label
Computational analysis platform
assay_families array · 9 items
[0]
meta_analysis
[1]
machine_learning
[2]
survival_analysis
[3]
statistical_regression
[4]
pca
[5]
molecular_docking
[6]
network_analysis
[7]
differential_expression
[8]
gwas
candidate
Automated Assays Laravel application and simulated adapters
gaps array · 0 items
readiness object · 8 fields
state
complete
tier
R1
blocked_on
nothing:replicable_now
axes object · 3 fields
method object · 5 fields
tier
R1
expressible
true
required_operations array · 4 items
[0]
group_summary
[1]
welch_t
[2]
bootstrap_mean_difference
[3]
group_comparison_anova
missing_operations array · 0 items
basis
The paper names the method it used and the corpus's method extractor maps it onto the DSL catalogue: anova.
capability object · 4 fields
tier
R1
capability_id
capability:computational_analysis
availability_state
owned
basis
The computational analysis is owned. The physical bench the paper used is not, so a physical validation cannot be run here.
data object · 6 fields
tier
R1
reachable
true
accessions array · 3 items
[0]
GSE98918
[1]
GSE178557
[2]
GSE216651
resolved_accessions array · 3 items
[0]
GSE98918
[1]
GSE178557
[2]
GSE216651
statements array · 1 item
[0]
The datasets used in this study are publicly accessible. The datasets included in this study can be downloaded from the GEO database (GSE98918: https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE98918; GSE178557: https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE178557), whose corresponding data are cited in references [18, 19]. Further inquiries can be directed to the corresponding author.
basis
The paper names GSE98918, GSE178557, GSE216651 in GEO database and the accession resolves in the repository. No dataset was downloaded and no licence was read.
can_run object · 3 fields
dsl_operations array · 4 items
[0]
group_summary
[1]
welch_t
[2]
bootstrap_mean_difference
[3]
group_comparison_anova
assets array · 2 items
[0]
source:pmid:40797087
[1]
data:geo:GSE178557
steps array · 1 item
[0]
run_analysis
must_build object · 5 fields
dsl_operations array · 0 items
converters array · 0 items
readers array · 0 items
capabilities array · 0 items
data_gaps array · 1 item
[0]
data:geo:GSE178557
gaps array · 0 items
review object · 5 fields
state
partial
machine_critique object · 5 fields
kind
extraction_review
reader object · 5 fields
model
MiniMax-M3.1-Flash
provider
minimax
provider_family
minimax
read_at
2026-11-01T19:59:15Z
independence
single_reader
evidence_check object · 2 fields
method
verbatim
availability
verbatim
calls
5
usage object · 3 fields
prompt_tokens
16913
completion_tokens
2998
cached_tokens
264
stages array · 1 item
[0] object · 4 fields
id
extraction
state
complete
reader
MiniMax-M3.1-Flash
provider
minimax
gaps array · 3 items
[0]
review.independent_reader
[1]
review.machine_critique
[2]
review.human_critique
execution object · 5 fields
state
absent
status
not_run
mode
null
runs array · 0 items
gaps array · 1 item
[0]
execution.not_run
provenance object · 7 fields
entities array · 3 items
[0] object · 3 fields
id
pmid:40797087
type
paper
label
pmid:40797087
[1] object · 3 fields
id
source:pmid:40797087
type
manuscript
label
PMID 40797087 full text
[2] object · 3 fields
id
data:geo:GSE178557
type
dataset
label
GEO GSE178557
activities array · 3 items
[0] object · 4 fields
id
activity-reading-sci-2026-11-01
type
classification
used array · 3 items
[0] object · 3 fields
id
pmid:40797087
type
paper
label
pmid:40797087
[1] object · 3 fields
id
source:pmid:40797087
type
manuscript
label
PMID 40797087 full text
[2] object · 3 fields
id
data:geo:GSE178557
type
dataset
label
GEO GSE178557
agent
agent:corpus-assay-engine
[1] object · 4 fields
id
activity-read-40797087
type
extraction
used array · 1 item
[0]
source:pmid:40797087
agent
agent:minimax-reader
[2] object · 4 fields
id
activity-resolve-GSE178557
type
accession_resolution
used array · 1 item
[0]
data:geo:GSE178557
agent
agent:corpus-assay-engine
agents array · 2 items
[0] object · 3 fields
id
agent:corpus-assay-engine
type
software
label
Corpus assay engine
[1] object · 3 fields
id
agent:minimax-reader
type
software
label
MiniMax literature reader
source_run_id
reading-sci-2026-11-01
dsl_catalogue_fingerprint
343fb30756ba6ec3
capability_table_fingerprint
2cb3e42f047d2ecf
snapshot_id
ba34b49490d9bfaf
lineage object · 4 fields
parent_id
pmid:40797087
parent_hash
sha256:b882ac0a651fb5c40f842a30089375628696162d0a19ef622691d551833598f1
fork_of
null
gaps array · 10 items
[0]
asset:data:geo:GSE178557 licence not read
[1]
asset:data:geo:GSE178557 not downloaded
[2]
asset:data:geo:GSE216651 licence not read
[3]
asset:data:geo:GSE216651 not downloaded
[4]
asset:data:geo:GSE98918 licence not read
[5]
asset:data:geo:GSE98918 not downloaded
[6]
execution.not_run
[7]
review.human_critique
[8]
review.independent_reader
[9]
review.machine_critique
assays array · 7 items
[0] object · 11 fields
role
data_generation
definition_id
animal_model
definition_version
99e1195c7d6f
required_operations array · 0 items
support_state
partial
source_hashes object · 1 field
assay_lexicon
99e1195c7d6f
confidence
0.99
evidence array · 4 items
[0]
multiple bioinformatics analyses along with in vivo and in vitro experiments to elucidate the me
[1]
most likely therapeutic target. In vitro and in vivo experiments demonstrated that DHT IIA signif
[2]
essment via CIBERSORTx. OA was induced in SD rats using a high carbohydrate and fat diet, foll
[3]
ARγ, GPX4, and the apoptosis marker TUNEL in rat cartilage were evaluated using immunofluores
order_basis
paper_text_order:674
id
assay:1
[1] object · 11 fields
role
data_generation
definition_id
apoptosis_assay
definition_version
99e1195c7d6f
required_operations array · 0 items
support_state
partial
source_hashes object · 1 field
assay_lexicon
99e1195c7d6f
confidence
0.69
evidence array · 1 item
[0]
he expression levels of PPARγ, GPX4, and the apoptosis marker TUNEL in rat cartilage were evaluated
order_basis
paper_text_order:1280
id
assay:2
[2] object · 11 fields
role
data_generation
definition_version
99e1195c7d6f
required_operations array · 0 items
support_state
partial
source_hashes object · 1 field
assay_lexicon
99e1195c7d6f
confidence
0.99
evidence array · 2 items
[0]
were evaluated using immunofluorescence and immunohistochemistry. In an LPS-induced ATDC5 chondrocyte injury
[1]
TUNEL in rat cartilage were evaluated using immunofluorescence and immunohistochemistry. In an LPS-induced
order_basis
paper_text_order:1342
id
assay:3
[3] object · 11 fields
role
data_generation
definition_id
western_blot
definition_version
99e1195c7d6f
required_operations array · 0 items
support_state
partial
source_hashes object · 1 field
assay_lexicon
99e1195c7d6f
confidence
0.93
evidence array · 1 item
[0]
LPS-induced ATDC5 chondrocyte injury model, Western blotting was used to assess the expression of PPARγ,
order_basis
paper_text_order:1437
id
assay:4
[4] object · 11 fields
role
data_generation
definition_id
transfection
definition_version
99e1195c7d6f
required_operations array · 0 items
support_state
partial
source_hashes object · 1 field
assay_lexicon
99e1195c7d6f
confidence
0.85
evidence array · 1 item
[0]
on levels. Meanwhile computer simulated gene knockdown also laterally confirmed that PPARγ is a key
order_basis
paper_text_order:2278
id
assay:5
[5] object · 11 fields
role
data_generation
definition_id
cell_culture
definition_version
99e1195c7d6f
required_operations array · 0 items
support_state
partial
source_hashes object · 1 field
assay_lexicon
99e1195c7d6f
confidence
0.77
evidence array · 1 item
[0]
ed from the Chinese Academy of Sciences, was cultured in DMEM (G4511, Servicebio) supplemented with 1
order_basis
paper_text_order:4445
id
assay:6
[6] object · 11 fields
role
analysis
definition_id
group_comparison
definition_version
f2132e96ae6c7a4e
required_operations array · 4 items
[0]
group_summary
[1]
welch_t
[2]
bootstrap_mean_difference
[3]
group_comparison_anova
support_state
supported
source_hashes object · 1 field
dsl_catalogue
f2132e96ae6c7a4e
evidence array · 1 item
[0]
For data that met the normal distribution and variance chi-square, a one-way ANOVA was performed followed by multiple comparisons using Tukey’s post hoc test. For data that did not meet the assumption of normality, the Kruskal-Wallis H test was used. If significant differences were observed (p < 0.05), pairwise comparisons were performed using Dunn’s test with Bonferroni correction.
order_basis
consumes_earlier_output
id
assay:7
Complete file
{"sci_version": "1.2", "schema": "https://corpus.bntrg.co.uk/sci/1.0/sci.schema.json", "id": "pmid:40797087", "kind": "science-record", "revision": 4, "content_hash": "sha256:0255801004f6e247522ee06fa81956364844871c1223553d98a522e95c9f4eee", "created_at": "2026-11-01T20:30:53Z", "updated_at": "2026-11-01T22:57:00Z", "generator": {"name": "corpus-assay-engine", "run_id": "reading-sci-2026-11-01"}, "paper": {"state": "complete", "title": "Dehydrotanshinone II A alleviates osteoarthritis via activating PPARγ to inhibit ferroptosis in chondrocytes.", "doi": "10.1038/s41598-025-14896-y", "pmid": "40797087", "authors": ["Wenli Guan", "Fahu Yuan", "Xin Wang"], "journal": "Scientific reports", "year": 2025, "abstract": "Osteoarthritis (OA) is a prevalent chronic degenerative joint disease. Ferroptosis, an iron-dependent form of programmed cell death, has been implicated as a crucial contributor to OA progression. Simiao Powder, a classical traditional Chinese medicine formula, has been widely used in clinical practice to treat inflammatory diseases such as gout and OA. However, its regulatory effects on ferroptosis remain unclear. This study investigates whether Simiao Powder could alleviate OA by regulating ferroptosis and analyzes its underlying mechanisms. We integrated multiple bioinformatics analyses along with in vivo and in vitro experiments to elucidate the mechanism by which DHT IIA treats OA. Potential therapeutic targets of Simiao Powder were identified through the TCMSP and GEO databases, and their potential biological functions were evaluated using GO enrichment, ROC curve analysis, molecular docking, and immune infiltration assessment via CIBERSORTx. OA was induced in SD rats using a high carbohydrate and fat diet, followed by a 16-week intervention with DHT IIA. Histological staining, OARSI scoring, and cartilage thickness measurements were performed. The expression levels of PPARγ, GPX4, and the apoptosis marker TUNEL in rat cartilage were evaluated using immunofluorescence and immunohistochemistry. In an LPS-induced ATDC5 chondrocyte injury model, Western blotting was used to assess the expression of PPARγ, COL2A1, ACSL4, and MMP13. Furthermore, the scTenifoldKnk algorithm was applied to perform a virtual knockout of PPARγ based on the GSE216651 single-cell RNA-seq dataset to explore its downstream regulatory effects. Bioinformatics analysis identified five key genes (CDKN1A, HMOX1, DPP4, GJA1, and PPARγ), among which PPARγ and HMOX1 exhibited strong predictive potential with AUC values > 0.8. Molecular docking analysis revealed that DHT IIA exhibited the lowest binding energy with PPARγ (-8.15 kcal/mol), indicating it as the most likely therapeutic target. In vitro and in vivo experiments demonstrated that DHT IIA significantly upregulated PPARγ expression reduced ACSL4, MMP13 and TUNEL levels, increased COL2A1 and GPX4 expression levels. Meanwhile computer simulated gene knockdown also laterally confirmed that PPARγ is a key gene affecting ferroptosis and OA development. The study confirmed that DHT IIA could improve the articular cartilage structure of OA rats by elevating PPARγ and inhibiting ferroptosis. This study reveals that DHT IIA, the active ingredient of Simiao Powder, may alleviate OA by inhibiting ferroptosis through the activation of PPARγ. These findings provide a new molecular mechanism basis for the treatment of OA by Simiao Powder, as well as scientific support for the subsequent drug development and clinical applications.", "claims": [{"id": "claim-method", "statement": "For data that met the normal distribution and variance chi-square, a one-way ANOVA was performed followed by multiple comparisons using Tukey’s post hoc test. For data that did not meet the assumption of normality, the Kruskal-Wallis H test was used. If significant differences were observed (p < 0.05), pairwise comparisons were performed using Dunn’s test with Bonferroni correction.", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:40797087", "locator": "sections[20] \"Statistical analysis\" paragraph 2", "quote": "For data that met the normal distribution and variance chi-square, a one-way ANOVA was performed followed by multiple comparisons using Tukey’s post hoc test. For data that did not meet the assumption of normality, the Kruskal-Wallis H test was used. If significant differences were observed (p < 0.05), pairwise comparisons were performed using Dunn’s test with Bonferroni correction."}], "state": "complete"}, {"id": "claim-data-access", "statement": "The datasets used in this study are publicly accessible. The datasets included in this study can be downloaded from the GEO database (GSE98918: https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE98918; GSE178557: https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE178557), whose corresponding data are cited in references [18, 19]. Further inquiries can be directed to the corresponding author.", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:40797087", "locator": "sections[37] \"Data availability\" paragraph 2", "quote": "The datasets used in this study are publicly accessible. The datasets included in this study can be downloaded from the GEO database (GSE98918: https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE98918; GSE178557: https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE178557), whose corresponding data are cited in references [18, 19]. Further inquiries can be directed to the corresponding author."}], "state": "complete"}, {"id": "claim-target-result", "statement": "Bioinformatics analysis identified five key genes (CDKN1A, HMOX1, DPP4, GJA1, and PPARγ), among which PPARγ and HMOX1 exhibited strong predictive potential with AUC values > 0.8.", "kind": "qualitative", "target": null, "evidence": [{"asset": "source:pmid:40797087", "locator": "sections[0] \"Abstract\" paragraph 1", "quote": "Bioinformatics analysis identified five key genes (CDKN1A, HMOX1, DPP4, GJA1, and PPARγ), among which PPARγ and HMOX1 exhibited strong predictive potential with AUC values > 0.8."}], "state": "complete"}], "gaps": []}, "experiment": {"state": "complete", "objective": "Bioinformatics analysis identified five key genes (CDKN1A, HMOX1, DPP4, GJA1, and PPARγ), among which PPARγ and HMOX1 exhibited strong predictive potential with AUC values > 0.8.", "steps": [{"id": "read_published_estimate", "order": 1, "name": "Read the published estimate from the source", "kind": "other", "state": "complete", "blocked_on": null, "description": "The claim, method and evidence span published with the source article.", "duration_hours": null, "parameters": {}, "inputs": ["source:pmid:40797087"], "outputs": ["the published estimate and its evidence"], "instruments": [], "reagents": []}, {"id": "obtain_source_data", "order": 2, "name": "Obtain the source data from the named repository", "kind": "data-preparation", "state": "complete", "blocked_on": null, "description": "The GEO series accession resolves and its sample accessions are listed. This lane did not download the dataset or read its licence.", "duration_hours": null, "parameters": {}, "inputs": ["data:geo:GSE178557"], "outputs": ["the source data with its repository provenance"], "instruments": [], "reagents": []}, {"id": "run_analysis", "order": 3, "name": "Run the published analysis", "kind": "analysis", "state": "complete", "blocked_on": null, "description": "Apply the paper's statistical method to the resolved series and compare the result with the published target.", "duration_hours": null, "parameters": {}, "inputs": ["data:geo:GSE178557"], "outputs": ["the replicated result and its comparison"], "instruments": [], "reagents": []}], "materials": [], "instruments": [], "reagents": [], "conditions": {}, "gaps": []}, "data": {"state": "partial", "assets": [{"id": "source:pmid:40797087", "role": "manuscript", "format": "xml", "media_type": "application/xml", "uri": "https://doi.org/10.1038/s41598-025-14896-y", "sha256": "sha256:29af428334fd4e19f753b005ed5192c9869a2119eea1657810b575378c33774c", "bytes": 60027, "access": "open", "state": "resolved", "reader": null, "reader_status": "reader_required", "identifier": "10.1038/s41598-025-14896-y", "version": null, "note": "Full article fetched from PMC; the checksum covers the rendered section body, not the original XML bytes.", "structure": {"pmcid": "PMC12343851", "source": "europe_pmc_fulltext", "coverage": "whole_body", "text_hash_scope": "rendered_section_body"}}, {"id": "data:geo:GSE178557", "role": "raw", "format": "geo-series", "media_type": "application/vnd.ncbi.geo-series+json", "uri": "https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE178557", "sha256": null, "bytes": null, "access": "open", "state": "resolved", "reader": null, "reader_status": "reader_required", "identifier": "GSE178557", "version": null, "note": "The datasets used in this study are publicly accessible. The datasets included in this study can be downloaded from the GEO database (GSE98918: https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE98918; GSE178557: https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE178557), whose corresponding data are cited in references [18, 19]. Further inquiries can be directed to the corresponding author.", "structure": {"repository": "GEO", "access_route": "GEO accession URL", "access_statement_verbatim": "The datasets used in this study are publicly accessible. The datasets included in this study can be downloaded from the GEO database (GSE98918: https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE98918; GSE178557: https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE178557), whose corresponding data are cited in references [18, 19]. Further inquiries can be directed to the corresponding author.", "access_statement_kind": "data_availability_statement", "sample_accessions": ["GSM5393765", "GSM5393766", "GSM5393767", "GSM5393768", "GSM5393769", "GSM5393770", "GSM5393771", "GSM5393772"], "sample_count": 8, "group_sizes": null, "group_sizes_basis": null, "platform": "13497", "taxon": "Homo sapiens", "title": "Microarray identifies differentially expressed mRNAs of cartilages between osteoarthritis (OA) patients and control patients", "resolution_checked_at": "2026-11-01T19:09:46Z", "resolution_check": "identifier_resolution_only_no_download_no_licence_read", "downloaded": false, "licence_read": false}}, {"id": "data:geo:GSE216651", "role": "raw", "format": "geo-series", "media_type": "application/vnd.ncbi.geo-series+json", "uri": "https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE216651", "sha256": null, "bytes": null, "access": "open", "state": "resolved", "reader": null, "reader_status": "reader_required", "identifier": "GSE216651", "version": null, "note": "The datasets used in this study are publicly accessible. The datasets included in this study can be downloaded from the GEO database (GSE98918: https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE98918; GSE178557: https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE178557), whose corresponding data are cited in references [18, 19]. Further inquiries can be directed to the corresponding author.", "structure": {"repository": "GEO", "access_route": "GEO accession URL", "access_statement_verbatim": "The datasets used in this study are publicly accessible. The datasets included in this study can be downloaded from the GEO database (GSE98918: https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE98918; GSE178557: https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE178557), whose corresponding data are cited in references [18, 19]. Further inquiries can be directed to the corresponding author.", "access_statement_kind": "data_availability_statement", "sample_accessions": ["GSM6685302", "GSM6685303", "GSM6685304", "GSM6685305", "GSM6685306", "GSM6685307", "GSM6685308", "GSM6685309", "GSM6685310"], "sample_count": 9, "group_sizes": null, "group_sizes_basis": null, "platform": "24676", "taxon": "Homo sapiens", "title": "Single-cell atlas of human infrapatellar fat pad and synovium unravels mechanisms of osteoarthritis-induced joint pathology", "resolution_checked_at": "2026-11-01T20:16:08Z", "resolution_check": "identifier_resolution_only_no_download_no_licence_read", "downloaded": false, "licence_read": false}}, {"id": "data:geo:GSE98918", "role": "raw", "format": "geo-series", "media_type": "application/vnd.ncbi.geo-series+json", "uri": "https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE98918", "sha256": null, "bytes": null, "access": "open", "state": "resolved", "reader": null, "reader_status": "reader_required", "identifier": "GSE98918", "version": null, "note": "The datasets used in this study are publicly accessible. The datasets included in this study can be downloaded from the GEO database (GSE98918: https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE98918; GSE178557: https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE178557), whose corresponding data are cited in references [18, 19]. Further inquiries can be directed to the corresponding author.", "structure": {"repository": "GEO", "access_route": "GEO accession URL", "access_statement_verbatim": "The datasets used in this study are publicly accessible. The datasets included in this study can be downloaded from the GEO database (GSE98918: https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE98918; GSE178557: https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE178557), whose corresponding data are cited in references [18, 19]. Further inquiries can be directed to the corresponding author.", "access_statement_kind": "data_availability_statement", "sample_accessions": ["GSM2627518", "GSM2627519", "GSM2627520", "GSM2627521", "GSM2627522", "GSM2627523", "GSM2627524", "GSM2627525", "GSM2627526", "GSM2627527", "GSM2627528", "GSM2627529", "GSM2627530", "GSM2627531", "GSM2627532", "GSM2627533", "GSM2627534", "GSM2627535", "GSM2627536", "GSM2627537", "GSM2627538", "GSM2627539", "GSM2627540", "GSM2627541"], "sample_count": 24, "group_sizes": null, "group_sizes_basis": null, "platform": "20844", "taxon": "Homo sapiens", "title": "The Impact of Osteoarthritis on the Biology of the Meniscus:", "resolution_checked_at": "2026-11-01T17:30:42Z", "resolution_check": "identifier_resolution_only_no_download_no_licence_read", "downloaded": false, "licence_read": false}}], "gaps": ["asset:data:geo:GSE178557 not downloaded", "asset:data:geo:GSE178557 licence not read", "asset:data:geo:GSE216651 not downloaded", "asset:data:geo:GSE216651 licence not read", "asset:data:geo:GSE98918 not downloaded", "asset:data:geo:GSE98918 licence not read"]}, "analysis": {"state": "complete", "methods": [{"id": "method-1", "family": "group_comparison", "specific": "anova", "label": "Group comparison", "dsl_operations": ["group_summary", "welch_t", "bootstrap_mean_difference", "group_comparison_anova"], "missing_operations": [], "expressible": true, "parameters": {}, "data_shapes": ["two_or_more_groups_continuous"], "evidence": {"score": 1.0, "band": "verbatim", "quote": "For data that met the normal distribution and variance chi-square, a one-way ANOVA was performed followed by multiple comparisons using Tukey’s post hoc test. For data that did not meet the assumption of normality, the Kruskal-Wallis H test was used. If significant differences were observed (p < 0.05), pairwise comparisons were performed using Dunn’s test with Bonferroni correction."}}, {"id": "method-2", "family": "network_analysis", "specific": "pathway_enrichment", "label": "Network / pathway analysis", "dsl_operations": ["pathway_enrich"], "missing_operations": [], "expressible": true, "parameters": {}, "data_shapes": ["edge_list"], "evidence": {"score": 0.7, "band": "medium", "quote": "GO enrichment"}}, {"id": "method-3", "family": "diagnostic_evaluation", "specific": "roc", "label": "Diagnostic test evaluation", "dsl_operations": ["confusion_counts", "roc_curve", "sensitivity_specificity", "solve_confusion_matrix", "classification_metrics", "published_precision_envelope"], "missing_operations": [], "expressible": true, "parameters": {}, "data_shapes": ["reference_standard_and_test"], "evidence": {"score": 0.7, "band": "medium", "quote": "ROC curve"}}, {"id": "method-4", "family": "contingency_analysis", "specific": "chi_square", "label": "Categorical (contingency table) analysis", "dsl_operations": ["chi_square_test"], "missing_operations": [], "expressible": true, "parameters": {}, "data_shapes": ["categorical_cross_tabulation"], "evidence": {"score": 0.8, "band": "high", "quote": "chi-square"}}], "targets": [], "gaps": []}, "capability": {"state": "complete", "requirements": [{"capability_id": "capability:computational_analysis", "label": "Computational analysis platform", "assay_families": ["meta_analysis", "machine_learning", "survival_analysis", "statistical_regression", "pca", "molecular_docking", "network_analysis", "differential_expression", "gwas"], "availability_state": "owned", "tier_unlocked": "R1", "candidate": "Automated Assays Laravel application and simulated adapters"}], "gaps": []}, "readiness": {"state": "complete", "tier": "R1", "blocking_axis": "none", "blocked_on": "nothing:replicable_now", "axes": {"method": {"tier": "R1", "expressible": true, "required_operations": ["group_summary", "welch_t", "bootstrap_mean_difference", "group_comparison_anova"], "missing_operations": [], "basis": "The paper names the method it used and the corpus's method extractor maps it onto the DSL catalogue: anova."}, "capability": {"tier": "R1", "capability_id": "capability:computational_analysis", "availability_state": "owned", "basis": "The computational analysis is owned. The physical bench the paper used is not, so a physical validation cannot be run here."}, "data": {"tier": "R1", "reachable": true, "accessions": ["GSE98918", "GSE178557", "GSE216651"], "resolved_accessions": ["GSE98918", "GSE178557", "GSE216651"], "statements": ["The datasets used in this study are publicly accessible. The datasets included in this study can be downloaded from the GEO database (GSE98918: https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE98918; GSE178557: https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE178557), whose corresponding data are cited in references [18, 19]. Further inquiries can be directed to the corresponding author."], "basis": "The paper names GSE98918, GSE178557, GSE216651 in GEO database and the accession resolves in the repository. No dataset was downloaded and no licence was read."}}, "can_run": {"dsl_operations": ["group_summary", "welch_t", "bootstrap_mean_difference", "group_comparison_anova"], "assets": ["source:pmid:40797087", "data:geo:GSE178557"], "steps": ["run_analysis"]}, "must_build": {"dsl_operations": [], "converters": [], "readers": [], "capabilities": [], "data_gaps": ["data:geo:GSE178557"]}, "gaps": []}, "review": {"state": "partial", "machine_critique": {"kind": "extraction_review", "reader": {"model": "MiniMax-M3.1-Flash", "provider": "minimax", "provider_family": "minimax", "read_at": "2026-11-01T19:59:15Z", "independence": "single_reader"}, "evidence_check": {"method": "verbatim", "availability": "verbatim"}, "calls": 5, "usage": {"prompt_tokens": 16913, "completion_tokens": 2998, "cached_tokens": 264}}, "human_critique": null, "stages": [{"id": "extraction", "state": "complete", "reader": "MiniMax-M3.1-Flash", "provider": "minimax"}], "gaps": ["review.independent_reader", "review.machine_critique", "review.human_critique"]}, "execution": {"state": "absent", "status": "not_run", "mode": null, "runs": [], "gaps": ["execution.not_run"]}, "provenance": {"entities": [{"id": "pmid:40797087", "type": "paper", "label": "pmid:40797087"}, {"id": "source:pmid:40797087", "type": "manuscript", "label": "PMID 40797087 full text"}, {"id": "data:geo:GSE178557", "type": "dataset", "label": "GEO GSE178557"}], "activities": [{"id": "activity-reading-sci-2026-11-01", "type": "classification", "used": [{"id": "pmid:40797087", "type": "paper", "label": "pmid:40797087"}, {"id": "source:pmid:40797087", "type": "manuscript", "label": "PMID 40797087 full text"}, {"id": "data:geo:GSE178557", "type": "dataset", "label": "GEO GSE178557"}], "agent": "agent:corpus-assay-engine"}, {"id": "activity-read-40797087", "type": "extraction", "used": ["source:pmid:40797087"], "agent": "agent:minimax-reader"}, {"id": "activity-resolve-GSE178557", "type": "accession_resolution", "used": ["data:geo:GSE178557"], "agent": "agent:corpus-assay-engine"}], "agents": [{"id": "agent:corpus-assay-engine", "type": "software", "label": "Corpus assay engine"}, {"id": "agent:minimax-reader", "type": "software", "label": "MiniMax literature reader"}], "source_run_id": "reading-sci-2026-11-01", "dsl_catalogue_fingerprint": "343fb30756ba6ec3", "capability_table_fingerprint": "2cb3e42f047d2ecf", "snapshot_id": "ba34b49490d9bfaf"}, "lineage": {"parent_id": "pmid:40797087", "parent_hash": "sha256:b882ac0a651fb5c40f842a30089375628696162d0a19ef622691d551833598f1", "fork_of": null, "generation": 3}, "gaps": ["asset:data:geo:GSE178557 licence not read", "asset:data:geo:GSE178557 not downloaded", "asset:data:geo:GSE216651 licence not read", "asset:data:geo:GSE216651 not downloaded", "asset:data:geo:GSE98918 licence not read", "asset:data:geo:GSE98918 not downloaded", "execution.not_run", "review.human_critique", "review.independent_reader", "review.machine_critique"], "assays": [{"role": "data_generation", "definition_id": "animal_model", "definition_version": "99e1195c7d6f", "definition_digest": null, "required_operations": [], "support_state": "partial", "source_hashes": {"assay_lexicon": "99e1195c7d6f"}, "confidence": 0.99, "evidence": ["multiple bioinformatics analyses along with in vivo and in vitro experiments to elucidate the me", "most likely therapeutic target. In vitro and in vivo experiments demonstrated that DHT IIA signif", "essment via CIBERSORTx. OA was induced in SD rats using a high carbohydrate and fat diet, foll", "ARγ, GPX4, and the apoptosis marker TUNEL in rat cartilage were evaluated using immunofluores"], "order_basis": "paper_text_order:674", "id": "assay:1"}, {"role": "data_generation", "definition_id": "apoptosis_assay", "definition_version": "99e1195c7d6f", "definition_digest": null, "required_operations": [], "support_state": "partial", "source_hashes": {"assay_lexicon": "99e1195c7d6f"}, "confidence": 0.69, "evidence": ["he expression levels of PPARγ, GPX4, and the apoptosis marker TUNEL in rat cartilage were evaluated"], "order_basis": "paper_text_order:1280", "id": "assay:2"}, {"role": "data_generation", "definition_id": "ihc", "definition_version": "99e1195c7d6f", "definition_digest": null, "required_operations": [], "support_state": "partial", "source_hashes": {"assay_lexicon": "99e1195c7d6f"}, "confidence": 0.99, "evidence": ["were evaluated using immunofluorescence and immunohistochemistry. In an LPS-induced ATDC5 chondrocyte injury", "TUNEL in rat cartilage were evaluated using immunofluorescence and immunohistochemistry. In an LPS-induced"], "order_basis": "paper_text_order:1342", "id": "assay:3"}, {"role": "data_generation", "definition_id": "western_blot", "definition_version": "99e1195c7d6f", "definition_digest": null, "required_operations": [], "support_state": "partial", "source_hashes": {"assay_lexicon": "99e1195c7d6f"}, "confidence": 0.93, "evidence": ["LPS-induced ATDC5 chondrocyte injury model, Western blotting was used to assess the expression of PPARγ,"], "order_basis": "paper_text_order:1437", "id": "assay:4"}, {"role": "data_generation", "definition_id": "transfection", "definition_version": "99e1195c7d6f", "definition_digest": null, "required_operations": [], "support_state": "partial", "source_hashes": {"assay_lexicon": "99e1195c7d6f"}, "confidence": 0.85, "evidence": ["on levels. Meanwhile computer simulated gene knockdown also laterally confirmed that PPARγ is a key"], "order_basis": "paper_text_order:2278", "id": "assay:5"}, {"role": "data_generation", "definition_id": "cell_culture", "definition_version": "99e1195c7d6f", "definition_digest": null, "required_operations": [], "support_state": "partial", "source_hashes": {"assay_lexicon": "99e1195c7d6f"}, "confidence": 0.77, "evidence": ["ed from the Chinese Academy of Sciences, was cultured in DMEM (G4511, Servicebio) supplemented with 1"], "order_basis": "paper_text_order:4445", "id": "assay:6"}, {"role": "analysis", "definition_id": "group_comparison", "definition_version": "f2132e96ae6c7a4e", "definition_digest": null, "required_operations": ["group_summary", "welch_t", "bootstrap_mean_difference", "group_comparison_anova"], "support_state": "supported", "source_hashes": {"dsl_catalogue": "f2132e96ae6c7a4e"}, "confidence": 1.0, "evidence": ["For data that met the normal distribution and variance chi-square, a one-way ANOVA was performed followed by multiple comparisons using Tukey’s post hoc test. For data that did not meet the assumption of normality, the Kruskal-Wallis H test was used. If significant differences were observed (p < 0.05), pairwise comparisons were performed using Dunn’s test with Bonferroni correction."], "order_basis": "consumes_earlier_output", "id": "assay:7"}]}