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

pmid:36142823

GDF15 Contributes to Radioresistance by Mediating the EMT and Stemness of Breast Cancer Cells.

Xinrui Zhao · Xinglong Liu · Songling Hu · Yan Pan · Jianghong Zhang · Guomei Tai · Chunlin Shao

International journal of molecular sciences · 2022 doi:10.3390/ijms231810911

Paper

complete

Experiment

complete

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:36142823
kind
science-record
content_hash
sha256:3d3a904539e3ab2aa292ed88a0c303383f02d53ec5eeae98827f4cad3fab0d50
schema
https://corpus.bntrg.co.uk/sci/1.0/sci.schema.json
created_at
2026-11-01T18:15:25Z
updated_at
2026-11-01T22:07:37Z
generator object · 2 fields
name
corpus-assay-engine
run_id
reading-sci-2026-11-01
paper object · 10 fields
state
complete
title
GDF15 Contributes to Radioresistance by Mediating the EMT and Stemness of Breast Cancer Cells.
doi
10.3390/ijms231810911
pmid
36142823
authors array · 7 items
[0]
Xinrui Zhao
[1]
Xinglong Liu
[2]
Songling Hu
[3]
Yan Pan
[4]
Jianghong Zhang
[5]
Guomei Tai
[6]
Chunlin Shao
journal
International journal of molecular sciences
year
2022
abstract
Radiotherapy is one of the conventional methods for the clinical treatment of breast cancer. However, radioresistance has an adverse effect on the prognosis of breast cancer patients after radiotherapy. In this study, using bioinformatic analysis of GSE59732 and GSE59733 datasets in the Gene Expression Omnibus (GEO) database together with the prognosis database of breast cancer patients after radiotherapy, the GDF15 gene was screened out to be related to the poor prognosis of breast cancer after radiotherapy. Compared with radiosensitive parental breast cancer cells, breast cancer cells with acquired radioresistance exhibited a high level of GDF15 expression and enhanced epithelial-to-mesenchymal transition (EMT) properties of migration and invasion, as well as obvious stem-like traits, including the increases of mammosphere formation ability, the proportion of stem cells (CD44+ CD24- cells), and the expressions of stem cell-related markers (SOX2, NANOG). Moreover, knockdown of GDF15 sensitized the radioresistance cells to irradiation and significantly inhibited their EMT and stem-like traits, indicating that GDF15 promoted the radioresistance of breast cancer by enhancing the properties of EMT and stemness. Conclusively, GDF15 may be applicable as a novel prognosis-related biomarker and a potential therapeutic target for breast cancer radiotherapy.
claims array · 2 items
[0] object · 6 fields
id
claim-method
statement
A Student’s t-test was performed to compare the difference of independent groups, and the significant level was considered at p < 0.05.
kind
methodological
target
null
evidence array · 1 item
[0] object · 3 fields
asset
source:pmid:36142823
locator
sections[26] "4.16. Statistical Analysis" paragraph 2
quote
A Student’s t-test was performed to compare the difference of independent groups, and the significant level was considered at p < 0.05.
state
complete
[1] object · 6 fields
id
claim-data-access
statement
The data presented in this study are available on request from the corresponding author upon reasonable request.
kind
methodological
target
null
evidence array · 1 item
[0] object · 3 fields
asset
source:pmid:36142823
locator
sections[31] "Data Availability Statement" paragraph 2
quote
The data presented in this study are available on request from the corresponding author upon reasonable request.
state
complete
gaps array · 0 items
experiment object · 8 fields
state
complete
objective
The paper states no numerical result for the registered target in the specified sections.
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:36142823
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:GSE59732
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:GSE59732
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 · 3 items
[0] object · 15 fields
id
source:pmid:36142823
role
manuscript
format
xml
media_type
application/xml
uri
https://doi.org/10.3390/ijms231810911
sha256
sha256:c08ea29b2873bfd2c78e66433ae4e2de0bbe6fc4673b8edf1098a434f9dd1892
bytes
55527
access
open
state
resolved
reader
null
reader_status
reader_required
identifier
10.3390/ijms231810911
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
PMC9504016
source
europe_pmc_fulltext
coverage
whole_body
text_hash_scope
rendered_section_body
[1] object · 15 fields
id
data:geo:GSE59732
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=GSE59732
sha256
null
bytes
null
access
open
state
resolved
reader
null
reader_status
reader_required
identifier
GSE59732
version
null
note
The data presented in this study are available on request from the corresponding author upon reasonable request.
structure object · 15 fields
repository
GEO
access_route
GEO accession URL
access_statement_verbatim
The data presented in this study are available on request from the corresponding author upon reasonable request.
access_statement_kind
data_availability_statement
sample_accessions array · 96 items
[0]
GSM1444557
[1]
GSM1444558
[2]
GSM1444559
[3]
GSM1444560
[4]
GSM1444561
[5]
GSM1444562
[6]
GSM1444563
[7]
GSM1444564
[8]
GSM1444565
[9]
GSM1444566
[10]
GSM1444567
[11]
GSM1444568
[12]
GSM1444569
[13]
GSM1444570
[14]
GSM1444571
[15]
GSM1444572
[16]
GSM1444573
[17]
GSM1444574
[18]
GSM1444575
[19]
GSM1444576
[20]
GSM1444577
[21]
GSM1444578
[22]
GSM1444579
[23]
GSM1444580
[24]
GSM1444581
[25]
GSM1444582
[26]
GSM1444583
[27]
GSM1444584
[28]
GSM1444585
[29]
GSM1444586
[30]
GSM1444587
[31]
GSM1444588
[32]
GSM1444589
[33]
GSM1444590
[34]
GSM1444591
[35]
GSM1444592
[36]
GSM1444593
[37]
GSM1444594
[38]
GSM1444595
[39]
GSM1444596
[40]
GSM1444597
[41]
GSM1444598
[42]
GSM1444599
[43]
GSM1444600
[44]
GSM1444601
[45]
GSM1444602
[46]
GSM1444603
[47]
GSM1444604
[48]
GSM1444605
[49]
GSM1444606
[50]
GSM1444607
[51]
GSM1444608
[52]
GSM1444609
[53]
GSM1444610
[54]
GSM1444611
[55]
GSM1444612
[56]
GSM1444613
[57]
GSM1444614
[58]
GSM1444615
[59]
GSM1444616
[60]
GSM1444617
[61]
GSM1444618
[62]
GSM1444619
[63]
GSM1444620
[64]
GSM1444621
[65]
GSM1444622
[66]
GSM1444623
[67]
GSM1444624
[68]
GSM1444625
[69]
GSM1444626
[70]
GSM1444627
[71]
GSM1444628
[72]
GSM1444629
[73]
GSM1444630
[74]
GSM1444631
[75]
GSM1444632
[76]
GSM1444633
[77]
GSM1444634
[78]
GSM1444635
[79]
GSM1444636
[80]
GSM1444637
[81]
GSM1444638
[82]
GSM1444639
[83]
GSM1444640
[84]
GSM1444641
[85]
GSM1444642
[86]
GSM1444643
[87]
GSM1444644
[88]
GSM1444645
[89]
GSM1444646
[90]
GSM1444647
[91]
GSM1444648
[92]
GSM1444649
[93]
GSM1444650
[94]
GSM1444651
[95]
GSM1444652
sample_count
96
group_sizes
null
group_sizes_basis
null
platform
571
taxon
Homo sapiens
title
Gene expression profiling in response to radiation treatment in breast cancer [cell lines]
resolution_checked_at
2026-11-01T18:46:34Z
resolution_check
identifier_resolution_only_no_download_no_licence_read
downloaded
false
licence_read
false
[2] object · 15 fields
id
data:geo:GSE59733
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=GSE59733
sha256
null
bytes
null
access
open
state
resolved
reader
null
reader_status
reader_required
identifier
GSE59733
version
null
note
The data presented in this study are available on request from the corresponding author upon reasonable request.
structure object · 15 fields
repository
GEO
access_route
GEO accession URL
access_statement_verbatim
The data presented in this study are available on request from the corresponding author upon reasonable request.
access_statement_kind
data_availability_statement
sample_accessions array · 19 items
[0]
GSM1444653
[1]
GSM1444654
[2]
GSM1444655
[3]
GSM1444656
[4]
GSM1444657
[5]
GSM1444658
[6]
GSM1444659
[7]
GSM1444660
[8]
GSM1444661
[9]
GSM1444662
[10]
GSM1444663
[11]
GSM1444664
[12]
GSM1444665
[13]
GSM1444666
[14]
GSM1444667
[15]
GSM1444668
[16]
GSM1444669
[17]
GSM1444670
[18]
GSM1444671
sample_count
19
group_sizes
null
group_sizes_basis
null
platform
18990
taxon
Homo sapiens
title
Gene expression profiling in response to radiation treatment in breast cancer [patient samples]
resolution_checked_at
2026-11-01T18:46:34Z
resolution_check
identifier_resolution_only_no_download_no_licence_read
downloaded
false
licence_read
false
gaps array · 4 items
[0]
asset:data:geo:GSE59732 not downloaded
[1]
asset:data:geo:GSE59732 licence not read
[2]
asset:data:geo:GSE59733 not downloaded
[3]
asset:data:geo:GSE59733 licence not read
analysis object · 4 fields
state
partial
methods array · 3 items
[0] object · 10 fields
id
method-1
family
network_analysis
specific
ppi_network
label
Network / pathway analysis
dsl_operations array · 3 items
[0]
build_graph
[1]
centrality_scores
[2]
pathway_enrich
missing_operations array · 0 items
parameters object · 0 fields
data_shapes array · 1 item
[0]
edge_list
evidence object · 3 fields
score
0.8
band
high
quote
PPI
[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
0.8
band
high
quote
pathway enrichment
[2] object · 10 fields
id
method-3
family
null
specific
null
label
Student’s t-test
dsl_operations array · 0 items
missing_operations array · 0 items
parameters object · 0 fields
data_shapes array · 0 items
evidence object · 3 fields
score
1
band
verbatim
quote
A Student’s t-test was performed to compare the difference of independent groups, and the significant level was considered at p < 0.05.
targets array · 0 items
gaps array · 1 item
[0]
method.reader_named_unmapped
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 · 3 items
[0]
build_graph
[1]
centrality_scores
[2]
pathway_enrich
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: ppi_network.
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]
GSE59732
[1]
GSE59733
resolved_accessions array · 2 items
[0]
GSE59732
[1]
GSE59733
statements array · 1 item
[0]
The data presented in this study are available on request from the corresponding author upon reasonable request.
basis
The paper names GSE59732, GSE59733 in Gene Expression Omnibus (GEO) and the accession resolves in the repository. No dataset was downloaded and no licence was read.
can_run object · 3 fields
dsl_operations array · 3 items
[0]
build_graph
[1]
centrality_scores
[2]
pathway_enrich
assets array · 2 items
[0]
source:pmid:36142823
[1]
data:geo:GSE59732
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:GSE59732
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
2026-11-01T18:06:37Z
independence
single_reader
evidence_check object · 2 fields
method
verbatim
availability
verbatim
calls
5
usage object · 3 fields
prompt_tokens
17237
completion_tokens
2308
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:36142823
type
paper
label
pmid:36142823
[1] object · 3 fields
id
source:pmid:36142823
type
manuscript
label
PMID 36142823 full text
[2] object · 3 fields
id
data:geo:GSE59732
type
dataset
label
GEO GSE59732
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:36142823
type
paper
label
pmid:36142823
[1] object · 3 fields
id
source:pmid:36142823
type
manuscript
label
PMID 36142823 full text
[2] object · 3 fields
id
data:geo:GSE59732
type
dataset
label
GEO GSE59732
agent
agent:corpus-assay-engine
[1] object · 4 fields
id
activity-read-36142823
type
extraction
used array · 1 item
[0]
source:pmid:36142823
agent
agent:minimax-reader
[2] object · 4 fields
id
activity-resolve-GSE59732
type
accession_resolution
used array · 1 item
[0]
data:geo:GSE59732
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:36142823
parent_hash
sha256:f4b4e0ddb76393e02f5dc9d7f858a25199680aa1fc5aeb450f1c3ec30b368b10
fork_of
null
gaps array · 9 items
[0]
asset:data:geo:GSE59732 licence not read
[1]
asset:data:geo:GSE59732 not downloaded
[2]
asset:data:geo:GSE59733 licence not read
[3]
asset:data:geo:GSE59733 not downloaded
[4]
execution.not_run
[5]
method.reader_named_unmapped
[6]
review.human_critique
[7]
review.independent_reader
[8]
review.machine_critique
assays array · 4 items
[0] 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]
ell-related markers (SOX2, NANOG). Moreover, knockdown of GDF15 sensitized the radioresistance cell
order_basis
paper_text_order:1030
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 · 4 items
[0]
10% FBS and 1% penicillin/streptomycin. All cell lines were maintained in a humidified atmosphere containing 5% CO2
[1]
d, NY, USA). MCF-7 and MDA-MB-231 cells were cultured in Dulbecco’s modified Eagle’s medium (DMEM) su
[2]
treptomycin. T-47D and MDA-MB-468 cells were cultured in RPMI-1640 medium containing 10% FBS and 1% p
[3]
above 585 DEGs. (C) Venn diagrams of DEGs in MCF-7 and ZR751 cell lines from GSE59732 dataset a
order_basis
paper_text_order:2951
id
assay:2
[2] 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
0.99
evidence array · 2 items
[0]
dividual cancer stages of breast cancer. (G) Western blot assay of the GDF15 protein expression in MCF
[1]
7D, MDA-MB-23, MDA-MB-468). Judging from the Western blot assay, the expression of GDF15 was obviously
order_basis
paper_text_order:7432
id
assay:3
[3] object · 11 fields
role
analysis
definition_id
network_analysis
definition_version
f2132e96ae6c7a4e
required_operations array · 3 items
[0]
build_graph
[1]
centrality_scores
[2]
pathway_enrich
support_state
supported
source_hashes object · 1 field
dsl_catalogue
f2132e96ae6c7a4e
evidence array · 1 item
[0]
PPI
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:36142823", "kind": "science-record", "revision": 4, "content_hash": "sha256:3d3a904539e3ab2aa292ed88a0c303383f02d53ec5eeae98827f4cad3fab0d50", "created_at": "2026-11-01T18:15:25Z", "updated_at": "2026-11-01T22:07:37Z", "generator": {"name": "corpus-assay-engine", "run_id": "reading-sci-2026-11-01"}, "paper": {"state": "complete", "title": "GDF15 Contributes to Radioresistance by Mediating the EMT and Stemness of Breast Cancer Cells.", "doi": "10.3390/ijms231810911", "pmid": "36142823", "authors": ["Xinrui Zhao", "Xinglong Liu", "Songling Hu", "Yan Pan", "Jianghong Zhang", "Guomei Tai", "Chunlin Shao"], "journal": "International journal of molecular sciences", "year": 2022, "abstract": "Radiotherapy is one of the conventional methods for the clinical treatment of breast cancer. However, radioresistance has an adverse effect on the prognosis of breast cancer patients after radiotherapy. In this study, using bioinformatic analysis of GSE59732 and GSE59733 datasets in the Gene Expression Omnibus (GEO) database together with the prognosis database of breast cancer patients after radiotherapy, the GDF15 gene was screened out to be related to the poor prognosis of breast cancer after radiotherapy. Compared with radiosensitive parental breast cancer cells, breast cancer cells with acquired radioresistance exhibited a high level of GDF15 expression and enhanced epithelial-to-mesenchymal transition (EMT) properties of migration and invasion, as well as obvious stem-like traits, including the increases of mammosphere formation ability, the proportion of stem cells (CD44+ CD24- cells), and the expressions of stem cell-related markers (SOX2, NANOG). Moreover, knockdown of GDF15 sensitized the radioresistance cells to irradiation and significantly inhibited their EMT and stem-like traits, indicating that GDF15 promoted the radioresistance of breast cancer by enhancing the properties of EMT and stemness. Conclusively, GDF15 may be applicable as a novel prognosis-related biomarker and a potential therapeutic target for breast cancer radiotherapy.", "claims": [{"id": "claim-method", "statement": "A Student’s t-test was performed to compare the difference of independent groups, and the significant level was considered at p < 0.05.", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:36142823", "locator": "sections[26] \"4.16. Statistical Analysis\" paragraph 2", "quote": "A Student’s t-test was performed to compare the difference of independent groups, and the significant level was considered at p < 0.05."}], "state": "complete"}, {"id": "claim-data-access", "statement": "The data presented in this study are available on request from the corresponding author upon reasonable request.", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:36142823", "locator": "sections[31] \"Data Availability Statement\" paragraph 2", "quote": "The data presented in this study are available on request from the corresponding author upon reasonable request."}], "state": "complete"}], "gaps": []}, "experiment": {"state": "complete", "objective": "The paper states no numerical result for the registered target in the specified sections.", "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:36142823"], "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:GSE59732"], "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:GSE59732"], "outputs": ["the replicated result and its comparison"], "instruments": [], "reagents": []}], "materials": [], "instruments": [], "reagents": [], "conditions": {}, "gaps": []}, "data": {"state": "partial", "assets": [{"id": "source:pmid:36142823", "role": "manuscript", "format": "xml", "media_type": "application/xml", "uri": "https://doi.org/10.3390/ijms231810911", "sha256": "sha256:c08ea29b2873bfd2c78e66433ae4e2de0bbe6fc4673b8edf1098a434f9dd1892", "bytes": 55527, "access": "open", "state": "resolved", "reader": null, "reader_status": "reader_required", "identifier": "10.3390/ijms231810911", "version": null, "note": "Full article fetched from PMC; the checksum covers the rendered section body, not the original XML bytes.", "structure": {"pmcid": "PMC9504016", "source": "europe_pmc_fulltext", "coverage": "whole_body", "text_hash_scope": "rendered_section_body"}}, {"id": "data:geo:GSE59732", "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=GSE59732", "sha256": null, "bytes": null, "access": "open", "state": "resolved", "reader": null, "reader_status": "reader_required", "identifier": "GSE59732", "version": null, "note": "The data presented in this study are available on request from the corresponding author upon reasonable request.", "structure": {"repository": "GEO", "access_route": "GEO accession URL", "access_statement_verbatim": "The data presented in this study are available on request from the corresponding author upon reasonable request.", "access_statement_kind": "data_availability_statement", "sample_accessions": ["GSM1444557", "GSM1444558", "GSM1444559", "GSM1444560", "GSM1444561", "GSM1444562", "GSM1444563", "GSM1444564", "GSM1444565", "GSM1444566", "GSM1444567", "GSM1444568", "GSM1444569", "GSM1444570", "GSM1444571", "GSM1444572", "GSM1444573", "GSM1444574", "GSM1444575", "GSM1444576", "GSM1444577", "GSM1444578", "GSM1444579", "GSM1444580", "GSM1444581", "GSM1444582", "GSM1444583", "GSM1444584", "GSM1444585", "GSM1444586", "GSM1444587", "GSM1444588", "GSM1444589", "GSM1444590", "GSM1444591", "GSM1444592", "GSM1444593", "GSM1444594", "GSM1444595", "GSM1444596", "GSM1444597", "GSM1444598", "GSM1444599", "GSM1444600", "GSM1444601", "GSM1444602", "GSM1444603", "GSM1444604", "GSM1444605", "GSM1444606", "GSM1444607", "GSM1444608", "GSM1444609", "GSM1444610", "GSM1444611", "GSM1444612", "GSM1444613", "GSM1444614", "GSM1444615", "GSM1444616", "GSM1444617", "GSM1444618", "GSM1444619", "GSM1444620", "GSM1444621", "GSM1444622", "GSM1444623", "GSM1444624", "GSM1444625", "GSM1444626", "GSM1444627", "GSM1444628", "GSM1444629", "GSM1444630", "GSM1444631", "GSM1444632", "GSM1444633", "GSM1444634", "GSM1444635", "GSM1444636", "GSM1444637", "GSM1444638", "GSM1444639", "GSM1444640", "GSM1444641", "GSM1444642", "GSM1444643", "GSM1444644", "GSM1444645", "GSM1444646", "GSM1444647", "GSM1444648", "GSM1444649", "GSM1444650", "GSM1444651", "GSM1444652"], "sample_count": 96, "group_sizes": null, "group_sizes_basis": null, "platform": "571", "taxon": "Homo sapiens", "title": "Gene expression profiling in response to radiation treatment in breast cancer [cell lines]", "resolution_checked_at": "2026-11-01T18:46:34Z", "resolution_check": "identifier_resolution_only_no_download_no_licence_read", "downloaded": false, "licence_read": false}}, {"id": "data:geo:GSE59733", "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=GSE59733", "sha256": null, "bytes": null, "access": "open", "state": "resolved", "reader": null, "reader_status": "reader_required", "identifier": "GSE59733", "version": null, "note": "The data presented in this study are available on request from the corresponding author upon reasonable request.", "structure": {"repository": "GEO", "access_route": "GEO accession URL", "access_statement_verbatim": "The data presented in this study are available on request from the corresponding author upon reasonable request.", "access_statement_kind": "data_availability_statement", "sample_accessions": ["GSM1444653", "GSM1444654", "GSM1444655", "GSM1444656", "GSM1444657", "GSM1444658", "GSM1444659", "GSM1444660", "GSM1444661", "GSM1444662", "GSM1444663", "GSM1444664", "GSM1444665", "GSM1444666", "GSM1444667", "GSM1444668", "GSM1444669", "GSM1444670", "GSM1444671"], "sample_count": 19, "group_sizes": null, "group_sizes_basis": null, "platform": "18990", "taxon": "Homo sapiens", "title": "Gene expression profiling in response to radiation treatment in breast cancer [patient samples]", "resolution_checked_at": "2026-11-01T18:46:34Z", "resolution_check": "identifier_resolution_only_no_download_no_licence_read", "downloaded": false, "licence_read": false}}], "gaps": ["asset:data:geo:GSE59732 not downloaded", "asset:data:geo:GSE59732 licence not read", "asset:data:geo:GSE59733 not downloaded", "asset:data:geo:GSE59733 licence not read"]}, "analysis": {"state": "partial", "methods": [{"id": "method-1", "family": "network_analysis", "specific": "ppi_network", "label": "Network / pathway analysis", "dsl_operations": ["build_graph", "centrality_scores", "pathway_enrich"], "missing_operations": [], "expressible": true, "parameters": {}, "data_shapes": ["edge_list"], "evidence": {"score": 0.8, "band": "high", "quote": "PPI"}}, {"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": 0.8, "band": "high", "quote": "pathway enrichment"}}, {"id": "method-3", "family": null, "specific": null, "label": "Student’s t-test", "dsl_operations": [], "missing_operations": [], "expressible": null, "parameters": {}, "data_shapes": [], "evidence": {"score": 1.0, "band": "verbatim", "quote": "A Student’s t-test was performed to compare the difference of independent groups, and the significant level was considered at p < 0.05."}}], "targets": [], "gaps": ["method.reader_named_unmapped"]}, "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": ["build_graph", "centrality_scores", "pathway_enrich"], "missing_operations": [], "basis": "The paper names the method it used and the corpus's method extractor maps it onto the DSL catalogue: ppi_network."}, "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": ["GSE59732", "GSE59733"], "resolved_accessions": ["GSE59732", "GSE59733"], "statements": ["The data presented in this study are available on request from the corresponding author upon reasonable request."], "basis": "The paper names GSE59732, GSE59733 in Gene Expression Omnibus (GEO) and the accession resolves in the repository. No dataset was downloaded and no licence was read."}}, "can_run": {"dsl_operations": ["build_graph", "centrality_scores", "pathway_enrich"], "assets": ["source:pmid:36142823", "data:geo:GSE59732"], "steps": ["run_analysis"]}, "must_build": {"dsl_operations": [], "converters": [], "readers": [], "capabilities": [], "data_gaps": ["data:geo:GSE59732"]}, "gaps": []}, "review": {"state": "partial", "machine_critique": {"kind": "extraction_review", "reader": {"model": "MiniMax-M3.1-Flash", "provider": "minimax", "provider_family": "minimax", "read_at": "2026-11-01T18:06:37Z", "independence": "single_reader"}, "evidence_check": {"method": "verbatim", "availability": "verbatim"}, "calls": 5, "usage": {"prompt_tokens": 17237, "completion_tokens": 2308, "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:36142823", "type": "paper", "label": "pmid:36142823"}, {"id": "source:pmid:36142823", "type": "manuscript", "label": "PMID 36142823 full text"}, {"id": "data:geo:GSE59732", "type": "dataset", "label": "GEO GSE59732"}], "activities": [{"id": "activity-reading-sci-2026-11-01", "type": "classification", "used": [{"id": "pmid:36142823", "type": "paper", "label": "pmid:36142823"}, {"id": "source:pmid:36142823", "type": "manuscript", "label": "PMID 36142823 full text"}, {"id": "data:geo:GSE59732", "type": "dataset", "label": "GEO GSE59732"}], "agent": "agent:corpus-assay-engine"}, {"id": "activity-read-36142823", "type": "extraction", "used": ["source:pmid:36142823"], "agent": "agent:minimax-reader"}, {"id": "activity-resolve-GSE59732", "type": "accession_resolution", "used": ["data:geo:GSE59732"], "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:36142823", "parent_hash": "sha256:f4b4e0ddb76393e02f5dc9d7f858a25199680aa1fc5aeb450f1c3ec30b368b10", "fork_of": null, "generation": 3}, "gaps": ["asset:data:geo:GSE59732 licence not read", "asset:data:geo:GSE59732 not downloaded", "asset:data:geo:GSE59733 licence not read", "asset:data:geo:GSE59733 not downloaded", "execution.not_run", "method.reader_named_unmapped", "review.human_critique", "review.independent_reader", "review.machine_critique"], "assays": [{"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": ["ell-related markers (SOX2, NANOG). Moreover, knockdown of GDF15 sensitized the radioresistance cell"], "order_basis": "paper_text_order:1030", "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": ["10% FBS and 1% penicillin/streptomycin. All cell lines were maintained in a humidified atmosphere containing 5% CO2", "d, NY, USA). MCF-7 and MDA-MB-231 cells were cultured in Dulbecco’s modified Eagle’s medium (DMEM) su", "treptomycin. T-47D and MDA-MB-468 cells were cultured in RPMI-1640 medium containing 10% FBS and 1% p", "above 585 DEGs. (C) Venn diagrams of DEGs in MCF-7 and ZR751 cell lines from GSE59732 dataset a"], "order_basis": "paper_text_order:2951", "id": "assay:2"}, {"role": "data_generation", "definition_id": "western_blot", "definition_version": "99e1195c7d6f", "definition_digest": null, "required_operations": [], "support_state": "partial", "source_hashes": {"assay_lexicon": "99e1195c7d6f"}, "confidence": 0.99, "evidence": ["dividual cancer stages of breast cancer. (G) Western blot assay of the GDF15 protein expression in MCF", "7D, MDA-MB-23, MDA-MB-468). Judging from the Western blot assay, the expression of GDF15 was obviously"], "order_basis": "paper_text_order:7432", "id": "assay:3"}, {"role": "analysis", "definition_id": "network_analysis", "definition_version": "f2132e96ae6c7a4e", "definition_digest": null, "required_operations": ["build_graph", "centrality_scores", "pathway_enrich"], "support_state": "supported", "source_hashes": {"dsl_catalogue": "f2132e96ae6c7a4e"}, "confidence": 0.8, "evidence": ["PPI"], "order_basis": "consumes_earlier_output", "id": "assay:4"}]}