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

pmid:41444216

HDAC6 deficiency exacerbates atherosclerosis via STAT3-K685 acetylation-mediated CD36/SR-A upregulation in macrophages.

Wenqing Wang · Yue Jiang · Xuan Pan · Dong Chen · Hui Yang · Wang Pan · Mingjie Pan · Bin Wang

Cell death & disease · 2025 doi:10.1038/s41419-025-08344-y

Paper

complete

Experiment

partial

Data

partial

Analysis

partial

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:41444216
kind
science-record
content_hash
sha256:9174d20ef4a0ea36c3cf2965ee8550e688cf6707608b0811c8ffc1a45acd43e1
schema
https://corpus.bntrg.co.uk/sci/1.0/sci.schema.json
created_at
2026-11-01T20:31:25Z
updated_at
2026-11-01T22:57:38Z
generator object · 2 fields
name
corpus-assay-engine
run_id
reading-sci-2026-11-01
paper object · 10 fields
state
complete
title
HDAC6 deficiency exacerbates atherosclerosis via STAT3-K685 acetylation-mediated CD36/SR-A upregulation in macrophages.
doi
10.1038/s41419-025-08344-y
pmid
41444216
authors array · 8 items
[0]
Wenqing Wang
[1]
Yue Jiang
[2]
Xuan Pan
[3]
Dong Chen
[4]
Hui Yang
[5]
Wang Pan
[6]
Mingjie Pan
[7]
Bin Wang
journal
Cell death & disease
year
2025
abstract
Atherosclerosis (AS) is a prevalent chronic arterial disease characterized by excessive cholesterol accumulation in the arterial intima. While substantial progress has been made in elucidating its risk factors and pathogenesis, the upstream signaling molecules that drive the initiation and progression of AS remain poorly understood. Analysis of monocyte samples from the GSE23746 database revealed that Histone Deacetylase 6 (HDAC6) expression was significantly downregulated in patients with carotid atherosclerosis compared to healthy controls. In vitro experiments further demonstrated that HDAC6 deficiency markedly promotes foam cell formation in macrophages, a process dependent on its deacetylase activity. Mechanistically, HDAC6 interacts with signal transducer and activator of transcription 3 (STAT3) and regulates its acetylation at K685, a critical modification that facilitates macrophage foam cell formation. Specifically, the loss of HDAC6-mediated deacetylation leads to increased STAT3-K685 acetylation, which in turn upregulates the expression of CD36 and SRA, thereby enhancing cholesterol uptake in macrophages. Our findings establish HDAC6 as a protective regulator in atherosclerosis, which maintains lipid metabolic homeostasis by modulating the STAT3-CD36/SR-A axis. We also observed that systemic HDAC6 knockout exacerbated atherosclerotic progression in high-fat diet-fed ApoE⁻/⁻mice, accompanied by increased monocyte/macrophage infiltration into plaques. Collectively, this study establishes HDAC6 as a potential therapeutic target for atherosclerosis intervention.
claims array · 2 items
[0] object · 6 fields
id
claim-method
statement
The differentially expressed genes were calculated by Student's t test. To evaluate the association between the gene expression and survival, we categorized the samples into two group by median of individual gene expression. The P value of trend was generated by the Cox regression model. Kaplan–Meier survival curves were drawn and compared among subgroups using Cox proportional hazard model.
kind
methodological
target
null
evidence array · 1 item
[0] object · 3 fields
asset
source:pmid:41444216
locator
sections[3] "The analyze of GEO databases" paragraph 2
quote
The differentially expressed genes were calculated by Student's t test. To evaluate the association between the gene expression and survival, we categorized the samples into two group by median of individual gene expression. The P value of trend was generated by the Cox regression model. Kaplan–Meier survival curves were drawn and compared among subgroups using Cox proportional hazard model.
state
complete
[1] object · 6 fields
id
claim-data-access
statement
The datasets GSE23746 and GSE21545 of atherosclerosis samples used in this study were all downloaded from the GEO database (https://www.ncbi.nlm.nih.gov/geo/). All other data are available from the corresponding author upon reasonable request.
kind
methodological
target
null
evidence array · 1 item
[0] object · 3 fields
asset
source:pmid:41444216
locator
sections[29] "Data availability" paragraph 2
quote
The datasets GSE23746 and GSE21545 of atherosclerosis samples used in this study were all downloaded from the GEO database (https://www.ncbi.nlm.nih.gov/geo/). All other data are available from the corresponding author upon reasonable request.
state
complete
gaps array · 0 items
experiment object · 8 fields
state
partial
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:41444216
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:GSE21545
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
blocked
blocked_on
method:student_t
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:GSE21545
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 · 1 item
[0]
step:run_analysis blocked on method:student_t
data object · 3 fields
state
partial
assets array · 3 items
[0] object · 15 fields
id
source:pmid:41444216
role
manuscript
format
xml
media_type
application/xml
uri
https://doi.org/10.1038/s41419-025-08344-y
sha256
sha256:fe2a0ce10e3b419a1cdb33df5f97a58d20a1279c0c82b8908f8e7fd24ab709c5
bytes
65773
access
open
state
resolved
reader
null
reader_status
reader_required
identifier
10.1038/s41419-025-08344-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
PMC12848014
source
europe_pmc_fulltext
coverage
whole_body
text_hash_scope
rendered_section_body
[1] object · 15 fields
id
data:geo:GSE21545
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=GSE21545
sha256
null
bytes
null
access
open
state
resolved
reader
null
reader_status
reader_required
identifier
GSE21545
version
null
note
The datasets GSE23746 and GSE21545 of atherosclerosis samples used in this study were all downloaded from the GEO database (https://www.ncbi.nlm.nih.gov/geo/). All other data are available from the corresponding author upon reasonable request.
structure object · 15 fields
repository
GEO
access_route
GEO accession URL
access_statement_verbatim
The datasets GSE23746 and GSE21545 of atherosclerosis samples used in this study were all downloaded from the GEO database (https://www.ncbi.nlm.nih.gov/geo/). All other data are available from the corresponding author upon reasonable request.
access_statement_kind
data_availability_statement
sample_accessions array · 223 items
[0]
GSM892518
[1]
GSM892519
[2]
GSM892520
[3]
GSM892521
[4]
GSM892522
[5]
GSM892523
[6]
GSM892524
[7]
GSM892525
[8]
GSM892526
[9]
GSM892527
[10]
GSM892528
[11]
GSM892529
[12]
GSM892530
[13]
GSM892531
[14]
GSM892532
[15]
GSM892533
[16]
GSM892534
[17]
GSM892535
[18]
GSM892536
[19]
GSM892537
[20]
GSM892538
[21]
GSM892539
[22]
GSM892540
[23]
GSM892541
[24]
GSM892542
[25]
GSM892543
[26]
GSM892544
[27]
GSM892545
[28]
GSM892546
[29]
GSM892547
[30]
GSM892548
[31]
GSM892549
[32]
GSM892550
[33]
GSM892551
[34]
GSM892552
[35]
GSM892553
[36]
GSM892554
[37]
GSM892555
[38]
GSM892556
[39]
GSM892557
[40]
GSM892558
[41]
GSM892559
[42]
GSM892560
[43]
GSM892561
[44]
GSM892562
[45]
GSM892563
[46]
GSM892564
[47]
GSM892565
[48]
GSM892566
[49]
GSM892567
[50]
GSM892568
[51]
GSM892569
[52]
GSM892570
[53]
GSM892571
[54]
GSM892572
[55]
GSM892573
[56]
GSM892574
[57]
GSM892575
[58]
GSM892576
[59]
GSM892577
[60]
GSM892578
[61]
GSM892579
[62]
GSM892580
[63]
GSM892581
[64]
GSM892582
[65]
GSM892583
[66]
GSM892584
[67]
GSM892585
[68]
GSM892586
[69]
GSM892587
[70]
GSM892588
[71]
GSM892589
[72]
GSM892590
[73]
GSM892591
[74]
GSM892592
[75]
GSM892593
[76]
GSM892594
[77]
GSM892595
[78]
GSM892596
[79]
GSM892597
[80]
GSM892598
[81]
GSM892599
[82]
GSM892600
[83]
GSM892601
[84]
GSM892602
[85]
GSM892603
[86]
GSM892604
[87]
GSM892605
[88]
GSM892606
[89]
GSM892607
[90]
GSM892608
[91]
GSM892609
[92]
GSM892610
[93]
GSM892611
[94]
GSM892612
[95]
GSM892613
[96]
GSM892614
[97]
GSM892615
[98]
GSM892616
[99]
GSM892617
[100]
GSM892618
[101]
GSM892619
[102]
GSM892620
[103]
GSM892621
[104]
GSM892622
[105]
GSM892623
[106]
GSM892624
[107]
GSM892625
[108]
GSM892626
[109]
GSM892627
[110]
GSM892628
[111]
GSM892629
[112]
GSM892630
[113]
GSM892631
[114]
GSM892632
[115]
GSM892633
[116]
GSM892634
[117]
GSM892635
[118]
GSM892636
[119]
GSM892637
[120]
GSM892638
[121]
GSM892639
[122]
GSM892640
[123]
GSM892641
[124]
GSM892642
[125]
GSM892643
[126]
GSM892644
[127]
GSM892645
[128]
GSM892646
[129]
GSM892647
[130]
GSM892648
[131]
GSM892649
[132]
GSM892650
[133]
GSM892651
[134]
GSM892652
[135]
GSM892653
[136]
GSM892654
[137]
GSM892655
[138]
GSM892656
[139]
GSM892657
[140]
GSM892658
[141]
GSM892659
[142]
GSM892660
[143]
GSM892661
[144]
GSM892662
[145]
GSM892663
[146]
GSM892664
[147]
GSM892665
[148]
GSM892666
[149]
GSM892667
[150]
GSM892668
[151]
GSM892669
[152]
GSM892670
[153]
GSM892671
[154]
GSM892672
[155]
GSM892673
[156]
GSM892674
[157]
GSM892675
[158]
GSM892676
[159]
GSM892677
[160]
GSM892678
[161]
GSM892679
[162]
GSM892680
[163]
GSM892681
[164]
GSM892682
[165]
GSM892683
[166]
GSM892684
[167]
GSM892685
[168]
GSM892686
[169]
GSM892687
[170]
GSM892688
[171]
GSM892689
[172]
GSM892690
[173]
GSM892691
[174]
GSM892692
[175]
GSM892693
[176]
GSM892694
[177]
GSM892695
[178]
GSM892696
[179]
GSM892697
[180]
GSM892698
[181]
GSM892699
[182]
GSM892700
[183]
GSM892701
[184]
GSM892702
[185]
GSM892703
[186]
GSM892704
[187]
GSM892705
[188]
GSM892706
[189]
GSM892707
[190]
GSM892708
[191]
GSM892709
[192]
GSM892710
[193]
GSM892711
[194]
GSM892712
[195]
GSM892713
[196]
GSM892714
[197]
GSM892715
[198]
GSM892716
[199]
GSM892717
[200]
GSM892718
[201]
GSM892719
[202]
GSM892720
[203]
GSM892721
[204]
GSM892722
[205]
GSM892723
[206]
GSM892724
[207]
GSM892725
[208]
GSM892726
[209]
GSM892727
[210]
GSM892728
[211]
GSM892729
[212]
GSM892730
[213]
GSM892731
[214]
GSM892732
[215]
GSM892733
[216]
GSM892734
[217]
GSM892735
[218]
GSM892736
[219]
GSM892737
[220]
GSM892738
[221]
GSM892739
[222]
GSM892740
sample_count
223
group_sizes
null
group_sizes_basis
null
platform
570
taxon
Homo sapiens
title
Biobank of Karolinska Endarterectomy (BiKE)
resolution_checked_at
2026-11-01T15:39:54Z
resolution_check
identifier_resolution_only_no_download_no_licence_read
downloaded
false
licence_read
false
[2] object · 15 fields
id
data:geo:GSE23746
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=GSE23746
sha256
null
bytes
null
access
open
state
resolved
reader
null
reader_status
reader_required
identifier
GSE23746
version
null
note
The datasets GSE23746 and GSE21545 of atherosclerosis samples used in this study were all downloaded from the GEO database (https://www.ncbi.nlm.nih.gov/geo/). All other data are available from the corresponding author upon reasonable request.
structure object · 15 fields
repository
GEO
access_route
GEO accession URL
access_statement_verbatim
The datasets GSE23746 and GSE21545 of atherosclerosis samples used in this study were all downloaded from the GEO database (https://www.ncbi.nlm.nih.gov/geo/). All other data are available from the corresponding author upon reasonable request.
access_statement_kind
data_availability_statement
sample_accessions array · 95 items
[0]
GSM585942
[1]
GSM585943
[2]
GSM585944
[3]
GSM585945
[4]
GSM585946
[5]
GSM585947
[6]
GSM585948
[7]
GSM585949
[8]
GSM585950
[9]
GSM585951
[10]
GSM585952
[11]
GSM585953
[12]
GSM585954
[13]
GSM585955
[14]
GSM585956
[15]
GSM585957
[16]
GSM585958
[17]
GSM585959
[18]
GSM585960
[19]
GSM585961
[20]
GSM585962
[21]
GSM585963
[22]
GSM585964
[23]
GSM585965
[24]
GSM585966
[25]
GSM585967
[26]
GSM585968
[27]
GSM585969
[28]
GSM585970
[29]
GSM585971
[30]
GSM585972
[31]
GSM585973
[32]
GSM585974
[33]
GSM585975
[34]
GSM585976
[35]
GSM585977
[36]
GSM585978
[37]
GSM585979
[38]
GSM585980
[39]
GSM585981
[40]
GSM585982
[41]
GSM585983
[42]
GSM585984
[43]
GSM585985
[44]
GSM585986
[45]
GSM585987
[46]
GSM585988
[47]
GSM585989
[48]
GSM585990
[49]
GSM585991
[50]
GSM585992
[51]
GSM585993
[52]
GSM585994
[53]
GSM585995
[54]
GSM585996
[55]
GSM585997
[56]
GSM585998
[57]
GSM585999
[58]
GSM586000
[59]
GSM586001
[60]
GSM586002
[61]
GSM586003
[62]
GSM586004
[63]
GSM586005
[64]
GSM586006
[65]
GSM586007
[66]
GSM586008
[67]
GSM586009
[68]
GSM586010
[69]
GSM586011
[70]
GSM586012
[71]
GSM586013
[72]
GSM586014
[73]
GSM586015
[74]
GSM586016
[75]
GSM586017
[76]
GSM586018
[77]
GSM586019
[78]
GSM586020
[79]
GSM586021
[80]
GSM586022
[81]
GSM586023
[82]
GSM586024
[83]
GSM586025
[84]
GSM586026
[85]
GSM586027
[86]
GSM586028
[87]
GSM586029
[88]
GSM586030
[89]
GSM586031
[90]
GSM586032
[91]
GSM586033
[92]
GSM586034
[93]
GSM586035
[94]
GSM586036
sample_count
95
group_sizes
null
group_sizes_basis
null
platform
2700
taxon
Homo sapiens
title
Monocyte gene expression patterns distinguish subjects with and without atherosclerosis.
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 · 4 items
[0]
asset:data:geo:GSE21545 not downloaded
[1]
asset:data:geo:GSE21545 licence not read
[2]
asset:data:geo:GSE23746 not downloaded
[3]
asset:data:geo:GSE23746 licence not read
analysis object · 4 fields
state
partial
methods array · 3 items
[0] object · 10 fields
id
method-1
family
group_comparison
specific
student_t_test
label
Group comparison
dsl_operations array · 0 items
missing_operations array · 1 item
[0]
student_t
expressible
false
parameters object · 0 fields
data_shapes array · 1 item
[0]
two_or_more_groups_continuous
evidence object · 3 fields
score
1
band
verbatim
quote
The differentially expressed genes were calculated by Student's t test. To evaluate the association between the gene expression and survival, we categorized the samples into two group by median of individual gene expression. The P value of trend was generated by the Cox regression model. Kaplan–Meier survival curves were drawn and compared among subgroups using Cox proportional hazard model.
[1] object · 10 fields
id
method-2
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
0.8
band
high
quote
analysis of variance
[2] object · 10 fields
id
method-3
family
survival_analysis
specific
cox_proportional_hazards
label
Survival analysis
dsl_operations array · 1 item
[0]
cox_ph
missing_operations array · 0 items
parameters object · 1 field
p_value
The P value of trend was generated
data_shapes array · 1 item
[0]
time_to_event_with_censoring
evidence object · 3 fields
score
0.8
band
high
quote
Cox regression
targets array · 0 items
gaps array · 1 item
[0]
method.student_t
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
false
required_operations array · 0 items
missing_operations array · 1 item
[0]
student_t
basis
The paper names the method it used and the corpus's method extractor maps it onto the DSL catalogue: student_t_test.
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 · 2 items
[0]
GSE23746
[1]
GSE21545
resolved_accessions array · 2 items
[0]
GSE23746
[1]
GSE21545
statements array · 1 item
[0]
The datasets GSE23746 and GSE21545 of atherosclerosis samples used in this study were all downloaded from the GEO database (https://www.ncbi.nlm.nih.gov/geo/). All other data are available from the corresponding author upon reasonable request.
basis
The paper names GSE23746, GSE21545 in Gene Expression Omnibus (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 · 0 items
assets array · 2 items
[0]
source:pmid:41444216
[1]
data:geo:GSE21545
steps array · 0 items
must_build object · 5 fields
dsl_operations array · 1 item
[0] object · 3 fields
operation
student_t
priority
null
converters array · 0 items
readers array · 0 items
capabilities array · 0 items
data_gaps array · 1 item
[0]
data:geo:GSE21545
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
2026-11-01T20:08:49Z
independence
single_reader
evidence_check object · 2 fields
method
verbatim
availability
verbatim
calls
5
usage object · 3 fields
prompt_tokens
18202
completion_tokens
1478
cached_tokens
256
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:41444216
type
paper
label
pmid:41444216
[1] object · 3 fields
id
source:pmid:41444216
type
manuscript
label
PMID 41444216 full text
[2] object · 3 fields
id
data:geo:GSE21545
type
dataset
label
GEO GSE21545
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:41444216
type
paper
label
pmid:41444216
[1] object · 3 fields
id
source:pmid:41444216
type
manuscript
label
PMID 41444216 full text
[2] object · 3 fields
id
data:geo:GSE21545
type
dataset
label
GEO GSE21545
agent
agent:corpus-assay-engine
[1] object · 4 fields
id
activity-read-41444216
type
extraction
used array · 1 item
[0]
source:pmid:41444216
agent
agent:minimax-reader
[2] object · 4 fields
id
activity-resolve-GSE21545
type
accession_resolution
used array · 1 item
[0]
data:geo:GSE21545
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:41444216
parent_hash
sha256:c11804f0195d8680dad76b79a2a2384162719c8e17c90e253e0ab47365f11bd1
fork_of
null
gaps array · 10 items
[0]
asset:data:geo:GSE21545 licence not read
[1]
asset:data:geo:GSE21545 not downloaded
[2]
asset:data:geo:GSE23746 licence not read
[3]
asset:data:geo:GSE23746 not downloaded
[4]
execution.not_run
[5]
method.student_t
[6]
review.human_critique
[7]
review.independent_reader
[8]
review.machine_critique
[9]
step:run_analysis blocked on method:student_t
assays array · 4 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]
e animal facility. HDAC6−/− mice and ApoE−/− mice were bred to generate ApoE−/−/HDAC6−/− mice. DNAs
[1]
E−/− (n = 14), and ApoE−/−/HDAC6−/− (n = 14) mice were fed with high-fat diet (HFD, containing 40%
[2]
is included in figure legends. Cell cultures Murine macrophage cell line Raw264.7 cells (TIB-71;
[3]
to generate ApoE−/−/HDAC6−/− mice. DNAs from mouse tails were extracted by the One Step Mouse G
order_basis
paper_text_order:2158
id
assay:1
[1] 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
0.99
evidence array · 3 items
[0]
midified incubator at 37 °C with 5% CO2. All cell lines were maintained in a mycoplasma-free state, and mycoplasma d
[1]
Table 3 of the Supplementary materials. All cell lines were maintained in a mycoplasma-free state. At the end of ea
[2]
ing. The results of mycoplasma detection for cultured cells are shown in Supplementary Fig. 2 of t
order_basis
paper_text_order:3736
id
assay:2
[2] 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
0.99
evidence array · 4 items
[0]
e using a lentiviral system. STAT3 siRNA was transfected into HDAC6 knockdown (KD) RAW264.7 cells usi
[1]
stem. STAT3 siRNA was transfected into HDAC6 knockdown (KD) RAW264.7 cells using Lipofectamine™ RNA
[2]
lts are shown in Supplementary Fig. 2. HDAC6 shRNA and STAT3 shRNA were transduced into the Raw
[3]
Supplementary Fig. 2. HDAC6 shRNA and STAT3 shRNA were transduced into the Raw264.7 cell line
order_basis
paper_text_order:3972
id
assay:3
[3] object · 11 fields
role
analysis
definition_id
group_comparison
definition_version
f2132e96ae6c7a4e
required_operations array · 0 items
support_state
partial
source_hashes object · 1 field
dsl_catalogue
f2132e96ae6c7a4e
evidence array · 1 item
[0]
The differentially expressed genes were calculated by Student's t test. To evaluate the association between the gene expression and survival, we categorized the samples into two group by median of individual gene expression. The P value of trend was generated by the Cox regression model. Kaplan–Meier survival curves were drawn and compared among subgroups using Cox proportional hazard model.
order_basis
consumes_earlier_output
id
assay:4
Complete file
{"sci_version": "1.2", "schema": "https://corpus.bntrg.co.uk/sci/1.0/sci.schema.json", "id": "pmid:41444216", "kind": "science-record", "revision": 4, "content_hash": "sha256:9174d20ef4a0ea36c3cf2965ee8550e688cf6707608b0811c8ffc1a45acd43e1", "created_at": "2026-11-01T20:31:25Z", "updated_at": "2026-11-01T22:57:38Z", "generator": {"name": "corpus-assay-engine", "run_id": "reading-sci-2026-11-01"}, "paper": {"state": "complete", "title": "HDAC6 deficiency exacerbates atherosclerosis via STAT3-K685 acetylation-mediated CD36/SR-A upregulation in macrophages.", "doi": "10.1038/s41419-025-08344-y", "pmid": "41444216", "authors": ["Wenqing Wang", "Yue Jiang", "Xuan Pan", "Dong Chen", "Hui Yang", "Wang Pan", "Mingjie Pan", "Bin Wang"], "journal": "Cell death & disease", "year": 2025, "abstract": "Atherosclerosis (AS) is a prevalent chronic arterial disease characterized by excessive cholesterol accumulation in the arterial intima. While substantial progress has been made in elucidating its risk factors and pathogenesis, the upstream signaling molecules that drive the initiation and progression of AS remain poorly understood. Analysis of monocyte samples from the GSE23746 database revealed that Histone Deacetylase 6 (HDAC6) expression was significantly downregulated in patients with carotid atherosclerosis compared to healthy controls. In vitro experiments further demonstrated that HDAC6 deficiency markedly promotes foam cell formation in macrophages, a process dependent on its deacetylase activity. Mechanistically, HDAC6 interacts with signal transducer and activator of transcription 3 (STAT3) and regulates its acetylation at K685, a critical modification that facilitates macrophage foam cell formation. Specifically, the loss of HDAC6-mediated deacetylation leads to increased STAT3-K685 acetylation, which in turn upregulates the expression of CD36 and SRA, thereby enhancing cholesterol uptake in macrophages. Our findings establish HDAC6 as a protective regulator in atherosclerosis, which maintains lipid metabolic homeostasis by modulating the STAT3-CD36/SR-A axis. We also observed that systemic HDAC6 knockout exacerbated atherosclerotic progression in high-fat diet-fed ApoE⁻/⁻mice, accompanied by increased monocyte/macrophage infiltration into plaques. Collectively, this study establishes HDAC6 as a potential therapeutic target for atherosclerosis intervention.", "claims": [{"id": "claim-method", "statement": "The differentially expressed genes were calculated by Student's t test. To evaluate the association between the gene expression and survival, we categorized the samples into two group by median of individual gene expression. The P value of trend was generated by the Cox regression model. Kaplan–Meier survival curves were drawn and compared among subgroups using Cox proportional hazard model.", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:41444216", "locator": "sections[3] \"The analyze of GEO databases\" paragraph 2", "quote": "The differentially expressed genes were calculated by Student's t test. To evaluate the association between the gene expression and survival, we categorized the samples into two group by median of individual gene expression. The P value of trend was generated by the Cox regression model. Kaplan–Meier survival curves were drawn and compared among subgroups using Cox proportional hazard model."}], "state": "complete"}, {"id": "claim-data-access", "statement": "The datasets GSE23746 and GSE21545 of atherosclerosis samples used in this study were all downloaded from the GEO database (https://www.ncbi.nlm.nih.gov/geo/). All other data are available from the corresponding author upon reasonable request.", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:41444216", "locator": "sections[29] \"Data availability\" paragraph 2", "quote": "The datasets GSE23746 and GSE21545 of atherosclerosis samples used in this study were all downloaded from the GEO database (https://www.ncbi.nlm.nih.gov/geo/). All other data are available from the corresponding author upon reasonable request."}], "state": "complete"}], "gaps": []}, "experiment": {"state": "partial", "objective": "", "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:41444216"], "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:GSE21545"], "outputs": ["the source data with its repository provenance"], "instruments": [], "reagents": []}, {"id": "run_analysis", "order": 3, "name": "Run the published analysis", "kind": "analysis", "state": "blocked", "blocked_on": "method:student_t", "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:GSE21545"], "outputs": ["the replicated result and its comparison"], "instruments": [], "reagents": []}], "materials": [], "instruments": [], "reagents": [], "conditions": {}, "gaps": ["step:run_analysis blocked on method:student_t"]}, "data": {"state": "partial", "assets": [{"id": "source:pmid:41444216", "role": "manuscript", "format": "xml", "media_type": "application/xml", "uri": "https://doi.org/10.1038/s41419-025-08344-y", "sha256": "sha256:fe2a0ce10e3b419a1cdb33df5f97a58d20a1279c0c82b8908f8e7fd24ab709c5", "bytes": 65773, "access": "open", "state": "resolved", "reader": null, "reader_status": "reader_required", "identifier": "10.1038/s41419-025-08344-y", "version": null, "note": "Full article fetched from PMC; the checksum covers the rendered section body, not the original XML bytes.", "structure": {"pmcid": "PMC12848014", "source": "europe_pmc_fulltext", "coverage": "whole_body", "text_hash_scope": "rendered_section_body"}}, {"id": "data:geo:GSE21545", "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=GSE21545", "sha256": null, "bytes": null, "access": "open", "state": "resolved", "reader": null, "reader_status": "reader_required", "identifier": "GSE21545", "version": null, "note": "The datasets GSE23746 and GSE21545 of atherosclerosis samples used in this study were all downloaded from the GEO database (https://www.ncbi.nlm.nih.gov/geo/). All other data are available from the corresponding author upon reasonable request.", "structure": {"repository": "GEO", "access_route": "GEO accession URL", "access_statement_verbatim": "The datasets GSE23746 and GSE21545 of atherosclerosis samples used in this study were all downloaded from the GEO database (https://www.ncbi.nlm.nih.gov/geo/). All other data are available from the corresponding author upon reasonable request.", "access_statement_kind": "data_availability_statement", "sample_accessions": ["GSM892518", "GSM892519", "GSM892520", "GSM892521", "GSM892522", "GSM892523", "GSM892524", "GSM892525", "GSM892526", "GSM892527", "GSM892528", "GSM892529", "GSM892530", "GSM892531", "GSM892532", "GSM892533", "GSM892534", "GSM892535", "GSM892536", "GSM892537", "GSM892538", "GSM892539", "GSM892540", "GSM892541", "GSM892542", "GSM892543", "GSM892544", "GSM892545", "GSM892546", "GSM892547", "GSM892548", "GSM892549", "GSM892550", "GSM892551", "GSM892552", "GSM892553", "GSM892554", "GSM892555", "GSM892556", "GSM892557", "GSM892558", "GSM892559", "GSM892560", "GSM892561", "GSM892562", "GSM892563", "GSM892564", "GSM892565", "GSM892566", "GSM892567", "GSM892568", "GSM892569", "GSM892570", "GSM892571", "GSM892572", "GSM892573", "GSM892574", "GSM892575", "GSM892576", "GSM892577", "GSM892578", "GSM892579", "GSM892580", "GSM892581", "GSM892582", "GSM892583", "GSM892584", "GSM892585", "GSM892586", "GSM892587", "GSM892588", "GSM892589", "GSM892590", "GSM892591", "GSM892592", "GSM892593", "GSM892594", "GSM892595", "GSM892596", "GSM892597", "GSM892598", "GSM892599", "GSM892600", "GSM892601", "GSM892602", "GSM892603", "GSM892604", "GSM892605", "GSM892606", "GSM892607", "GSM892608", "GSM892609", "GSM892610", "GSM892611", "GSM892612", "GSM892613", "GSM892614", "GSM892615", "GSM892616", "GSM892617", "GSM892618", "GSM892619", "GSM892620", "GSM892621", "GSM892622", "GSM892623", "GSM892624", "GSM892625", "GSM892626", "GSM892627", "GSM892628", "GSM892629", "GSM892630", "GSM892631", "GSM892632", "GSM892633", "GSM892634", "GSM892635", "GSM892636", "GSM892637", "GSM892638", "GSM892639", "GSM892640", "GSM892641", "GSM892642", "GSM892643", "GSM892644", "GSM892645", "GSM892646", "GSM892647", "GSM892648", "GSM892649", "GSM892650", "GSM892651", "GSM892652", "GSM892653", "GSM892654", "GSM892655", "GSM892656", "GSM892657", "GSM892658", "GSM892659", "GSM892660", "GSM892661", "GSM892662", "GSM892663", "GSM892664", "GSM892665", "GSM892666", "GSM892667", "GSM892668", "GSM892669", "GSM892670", "GSM892671", "GSM892672", "GSM892673", "GSM892674", "GSM892675", "GSM892676", "GSM892677", "GSM892678", "GSM892679", "GSM892680", "GSM892681", "GSM892682", "GSM892683", "GSM892684", "GSM892685", "GSM892686", "GSM892687", "GSM892688", "GSM892689", "GSM892690", "GSM892691", "GSM892692", "GSM892693", "GSM892694", "GSM892695", "GSM892696", "GSM892697", "GSM892698", "GSM892699", "GSM892700", "GSM892701", "GSM892702", "GSM892703", "GSM892704", "GSM892705", "GSM892706", "GSM892707", "GSM892708", "GSM892709", "GSM892710", "GSM892711", "GSM892712", "GSM892713", "GSM892714", "GSM892715", "GSM892716", "GSM892717", "GSM892718", "GSM892719", "GSM892720", "GSM892721", "GSM892722", "GSM892723", "GSM892724", "GSM892725", "GSM892726", "GSM892727", "GSM892728", "GSM892729", "GSM892730", "GSM892731", "GSM892732", "GSM892733", "GSM892734", "GSM892735", "GSM892736", "GSM892737", "GSM892738", "GSM892739", "GSM892740"], "sample_count": 223, "group_sizes": null, "group_sizes_basis": null, "platform": "570", "taxon": "Homo sapiens", "title": "Biobank of Karolinska Endarterectomy (BiKE)", "resolution_checked_at": "2026-11-01T15:39:54Z", "resolution_check": "identifier_resolution_only_no_download_no_licence_read", "downloaded": false, "licence_read": false}}, {"id": "data:geo:GSE23746", "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=GSE23746", "sha256": null, "bytes": null, "access": "open", "state": "resolved", "reader": null, "reader_status": "reader_required", "identifier": "GSE23746", "version": null, "note": "The datasets GSE23746 and GSE21545 of atherosclerosis samples used in this study were all downloaded from the GEO database (https://www.ncbi.nlm.nih.gov/geo/). All other data are available from the corresponding author upon reasonable request.", "structure": {"repository": "GEO", "access_route": "GEO accession URL", "access_statement_verbatim": "The datasets GSE23746 and GSE21545 of atherosclerosis samples used in this study were all downloaded from the GEO database (https://www.ncbi.nlm.nih.gov/geo/). All other data are available from the corresponding author upon reasonable request.", "access_statement_kind": "data_availability_statement", "sample_accessions": ["GSM585942", "GSM585943", "GSM585944", "GSM585945", "GSM585946", "GSM585947", "GSM585948", "GSM585949", "GSM585950", "GSM585951", "GSM585952", "GSM585953", "GSM585954", "GSM585955", "GSM585956", "GSM585957", "GSM585958", "GSM585959", "GSM585960", "GSM585961", "GSM585962", "GSM585963", "GSM585964", "GSM585965", "GSM585966", "GSM585967", "GSM585968", "GSM585969", "GSM585970", "GSM585971", "GSM585972", "GSM585973", "GSM585974", "GSM585975", "GSM585976", "GSM585977", "GSM585978", "GSM585979", "GSM585980", "GSM585981", "GSM585982", "GSM585983", "GSM585984", "GSM585985", "GSM585986", "GSM585987", "GSM585988", "GSM585989", "GSM585990", "GSM585991", "GSM585992", "GSM585993", "GSM585994", "GSM585995", "GSM585996", "GSM585997", "GSM585998", "GSM585999", "GSM586000", "GSM586001", "GSM586002", "GSM586003", "GSM586004", "GSM586005", "GSM586006", "GSM586007", "GSM586008", "GSM586009", "GSM586010", "GSM586011", "GSM586012", "GSM586013", "GSM586014", "GSM586015", "GSM586016", "GSM586017", "GSM586018", "GSM586019", "GSM586020", "GSM586021", "GSM586022", "GSM586023", "GSM586024", "GSM586025", "GSM586026", "GSM586027", "GSM586028", "GSM586029", "GSM586030", "GSM586031", "GSM586032", "GSM586033", "GSM586034", "GSM586035", "GSM586036"], "sample_count": 95, "group_sizes": null, "group_sizes_basis": null, "platform": "2700", "taxon": "Homo sapiens", "title": "Monocyte gene expression patterns distinguish subjects with and without atherosclerosis.", "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:GSE21545 not downloaded", "asset:data:geo:GSE21545 licence not read", "asset:data:geo:GSE23746 not downloaded", "asset:data:geo:GSE23746 licence not read"]}, "analysis": {"state": "partial", "methods": [{"id": "method-1", "family": "group_comparison", "specific": "student_t_test", "label": "Group comparison", "dsl_operations": [], "missing_operations": ["student_t"], "expressible": false, "parameters": {}, "data_shapes": ["two_or_more_groups_continuous"], "evidence": {"score": 1.0, "band": "verbatim", "quote": "The differentially expressed genes were calculated by Student's t test. To evaluate the association between the gene expression and survival, we categorized the samples into two group by median of individual gene expression. The P value of trend was generated by the Cox regression model. Kaplan–Meier survival curves were drawn and compared among subgroups using Cox proportional hazard model."}}, {"id": "method-2", "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": 0.8, "band": "high", "quote": "analysis of variance"}}, {"id": "method-3", "family": "survival_analysis", "specific": "cox_proportional_hazards", "label": "Survival analysis", "dsl_operations": ["cox_ph"], "missing_operations": [], "expressible": true, "parameters": {"p_value": "The P value of trend was generated"}, "data_shapes": ["time_to_event_with_censoring"], "evidence": {"score": 0.8, "band": "high", "quote": "Cox regression"}}], "targets": [], "gaps": ["method.student_t"]}, "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": false, "required_operations": [], "missing_operations": ["student_t"], "basis": "The paper names the method it used and the corpus's method extractor maps it onto the DSL catalogue: student_t_test."}, "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": ["GSE23746", "GSE21545"], "resolved_accessions": ["GSE23746", "GSE21545"], "statements": ["The datasets GSE23746 and GSE21545 of atherosclerosis samples used in this study were all downloaded from the GEO database (https://www.ncbi.nlm.nih.gov/geo/). All other data are available from the corresponding author upon reasonable request."], "basis": "The paper names GSE23746, GSE21545 in Gene Expression Omnibus (GEO) database and the accession resolves in the repository. No dataset was downloaded and no licence was read."}}, "can_run": {"dsl_operations": [], "assets": ["source:pmid:41444216", "data:geo:GSE21545"], "steps": []}, "must_build": {"dsl_operations": [{"operation": "student_t", "unlocks_papers": null, "priority": null}], "converters": [], "readers": [], "capabilities": [], "data_gaps": ["data:geo:GSE21545"]}, "gaps": []}, "review": {"state": "partial", "machine_critique": {"kind": "extraction_review", "reader": {"model": "MiniMax-M3.1-Flash", "provider": "minimax", "provider_family": "minimax", "read_at": "2026-11-01T20:08:49Z", "independence": "single_reader"}, "evidence_check": {"method": "verbatim", "availability": "verbatim"}, "calls": 5, "usage": {"prompt_tokens": 18202, "completion_tokens": 1478, "cached_tokens": 256}}, "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:41444216", "type": "paper", "label": "pmid:41444216"}, {"id": "source:pmid:41444216", "type": "manuscript", "label": "PMID 41444216 full text"}, {"id": "data:geo:GSE21545", "type": "dataset", "label": "GEO GSE21545"}], "activities": [{"id": "activity-reading-sci-2026-11-01", "type": "classification", "used": [{"id": "pmid:41444216", "type": "paper", "label": "pmid:41444216"}, {"id": "source:pmid:41444216", "type": "manuscript", "label": "PMID 41444216 full text"}, {"id": "data:geo:GSE21545", "type": "dataset", "label": "GEO GSE21545"}], "agent": "agent:corpus-assay-engine"}, {"id": "activity-read-41444216", "type": "extraction", "used": ["source:pmid:41444216"], "agent": "agent:minimax-reader"}, {"id": "activity-resolve-GSE21545", "type": "accession_resolution", "used": ["data:geo:GSE21545"], "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:41444216", "parent_hash": "sha256:c11804f0195d8680dad76b79a2a2384162719c8e17c90e253e0ab47365f11bd1", "fork_of": null, "generation": 3}, "gaps": ["asset:data:geo:GSE21545 licence not read", "asset:data:geo:GSE21545 not downloaded", "asset:data:geo:GSE23746 licence not read", "asset:data:geo:GSE23746 not downloaded", "execution.not_run", "method.student_t", "review.human_critique", "review.independent_reader", "review.machine_critique", "step:run_analysis blocked on method:student_t"], "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": ["e animal facility. HDAC6−/− mice and ApoE−/− mice were bred to generate ApoE−/−/HDAC6−/− mice. DNAs", "E−/− (n = 14), and ApoE−/−/HDAC6−/− (n = 14) mice were fed with high-fat diet (HFD, containing 40%", "is included in figure legends. Cell cultures Murine macrophage cell line Raw264.7 cells (TIB-71;", "to generate ApoE−/−/HDAC6−/− mice. DNAs from mouse tails were extracted by the One Step Mouse G"], "order_basis": "paper_text_order:2158", "id": "assay:1"}, {"role": "data_generation", "definition_id": "cell_culture", "definition_version": "99e1195c7d6f", "definition_digest": null, "required_operations": [], "support_state": "partial", "source_hashes": {"assay_lexicon": "99e1195c7d6f"}, "confidence": 0.99, "evidence": ["midified incubator at 37 °C with 5% CO2. All cell lines were maintained in a mycoplasma-free state, and mycoplasma d", "Table 3 of the Supplementary materials. All cell lines were maintained in a mycoplasma-free state. At the end of ea", "ing. The results of mycoplasma detection for cultured cells are shown in Supplementary Fig. 2 of t"], "order_basis": "paper_text_order:3736", "id": "assay:2"}, {"role": "data_generation", "definition_id": "transfection", "definition_version": "99e1195c7d6f", "definition_digest": null, "required_operations": [], "support_state": "partial", "source_hashes": {"assay_lexicon": "99e1195c7d6f"}, "confidence": 0.99, "evidence": ["e using a lentiviral system. STAT3 siRNA was transfected into HDAC6 knockdown (KD) RAW264.7 cells usi", "stem. STAT3 siRNA was transfected into HDAC6 knockdown (KD) RAW264.7 cells using Lipofectamine™ RNA", "lts are shown in Supplementary Fig. 2. HDAC6 shRNA and STAT3 shRNA were transduced into the Raw", "Supplementary Fig. 2. HDAC6 shRNA and STAT3 shRNA were transduced into the Raw264.7 cell line"], "order_basis": "paper_text_order:3972", "id": "assay:3"}, {"role": "analysis", "definition_id": "group_comparison", "definition_version": "f2132e96ae6c7a4e", "definition_digest": null, "required_operations": [], "support_state": "partial", "source_hashes": {"dsl_catalogue": "f2132e96ae6c7a4e"}, "confidence": 1.0, "evidence": ["The differentially expressed genes were calculated by Student's t test. To evaluate the association between the gene expression and survival, we categorized the samples into two group by median of individual gene expression. The P value of trend was generated by the Cox regression model. Kaplan–Meier survival curves were drawn and compared among subgroups using Cox proportional hazard model."], "order_basis": "consumes_earlier_output", "id": "assay:4"}]}