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

pmid:41208827

Collagen fibril formation at the plasma membrane occurs independently from collagen secretion.

Adam Pickard · Richa Garva · Antony Adamson · Ben C Calverley · Anna Hoyle · Christina E Hayward · David Spiller · Yinhui Lu · Nigel Hodson · Oriana Mandolfo · Kevin Kim · George Bou-Gharios · Joe Swift · Brian Bigger · Karl E Kadler

Wellcome open research · 2025 doi:10.12688/wellcomeopenres.23776.1

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:41208827
kind
science-record
content_hash
sha256:411a34088f7cbf6ce430645d8a6e47c6a499c2e645135ebf6e10381728a4fe30
schema
https://corpus.bntrg.co.uk/sci/1.0/sci.schema.json
created_at
2026-11-01T20:31:14Z
updated_at
2026-11-01T22:14:57Z
generator object · 2 fields
name
corpus-assay-engine
run_id
reading-sci-2026-11-01
paper object · 10 fields
state
complete
title
Collagen fibril formation at the plasma membrane occurs independently from collagen secretion.
doi
10.12688/wellcomeopenres.23776.1
pmid
41208827
authors array · 15 items
[0]
Adam Pickard
[1]
Richa Garva
[2]
Antony Adamson
[3]
Ben C Calverley
[4]
Anna Hoyle
[5]
Christina E Hayward
[6]
David Spiller
[7]
Yinhui Lu
[8]
Nigel Hodson
[9]
Oriana Mandolfo
[10]
Kevin Kim
[11]
George Bou-Gharios
[12]
Joe Swift
[13]
Brian Bigger
[14]
Karl E Kadler
journal
Wellcome open research
year
2025
abstract
Background: Collagen fibrils are the primary supporting scaffolds of vertebrate tissues, but the mechanism of assembly is unclear. Methods: Here, using CRISPR-tagging of type I collagen, high-resolution light imaging, and SILAC labelling, we elucidated the cellular mechanism underlying the spatiotemporal assembly of collagen fibrils in cultured fibroblasts. Results: Our findings reveal the multifaceted trafficking of collagen, including constitutive secretion, intracellular pooling, and plasma membrane-directed fibrillogenesis. Notably, we differentiated the processes of collagen secretion and fibril assembly and identified the crucial involvement of endocytosis in the regulation of fibril formation. By employing Col1a1 knockout fibroblasts, we demonstrated the incorporation of exogenous collagen into the nucleation sites at the plasma membrane through these recycling mechanisms. Conclusions: Our study sheds light on a complex and previously unidentified collagen assembly process and its regulation of health and disease. Mass spectrometry data were available via ProteomeXchange with the identifier PXD036794.
claims array · 2 items
[0] object · 6 fields
id
claim-method
statement
** represents p<0.01, Student’s T-test, unpaired.
kind
methodological
target
null
evidence array · 1 item
[0] object · 3 fields
asset
source:pmid:41208827
locator
sections[23] "Collagen fibril formation blocked in the presence of monensin but not brefeldin A" paragraph 3
quote
** represents p<0.01, Student’s T-test, unpaired.
state
complete
[1] object · 6 fields
id
claim-data-access
statement
ProteomeXchange: Consortium via the PRIDE partner repository: mass spectrometry proteomics data. Accession number PXD036794; https://dx.doi.org/10.6019/PXD036794 ( Perez-Riverol et al., 2022).
kind
methodological
target
null
evidence array · 1 item
[0] object · 3 fields
asset
source:pmid:41208827
locator
sections[29] "Underlying data" paragraph 2
quote
ProteomeXchange: Consortium via the PRIDE partner repository: mass spectrometry proteomics data. Accession number PXD036794; https://dx.doi.org/10.6019/PXD036794 ( Perez-Riverol et al., 2022).
state
complete
gaps array · 0 items
experiment object · 8 fields
state
complete
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:41208827
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:PXD036794
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:PXD036794
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 · 2 items
[0] object · 15 fields
id
source:pmid:41208827
role
manuscript
format
xml
media_type
application/xml
uri
https://doi.org/10.12688/wellcomeopenres.23776.1
sha256
sha256:68c6a532a62b20e5765e255dacee560ded1df850cb44a6318c245e15f5ffe93b
bytes
66899
access
open
state
resolved
reader
null
reader_status
reader_required
identifier
10.12688/wellcomeopenres.23776.1
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
PMC12595305
source
europe_pmc_fulltext
coverage
whole_body_without_references
text_hash_scope
rendered_section_body
[1] object · 15 fields
id
data:geo:PXD036794
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=PXD036794
sha256
null
bytes
null
access
open
state
resolved
reader
null
reader_status
reader_required
identifier
PXD036794
version
null
note
ProteomeXchange: Consortium via the PRIDE partner repository: mass spectrometry proteomics data. Accession number PXD036794; https://dx.doi.org/10.6019/PXD036794 ( Perez-Riverol et al., 2022).
structure object · 15 fields
repository
GEO
access_route
GEO accession URL
access_statement_verbatim
ProteomeXchange: Consortium via the PRIDE partner repository: mass spectrometry proteomics data. Accession number PXD036794; https://dx.doi.org/10.6019/PXD036794 ( Perez-Riverol et al., 2022).
access_statement_kind
repository_route_statement
sample_accessions array · 0 items
sample_count
null
group_sizes
null
group_sizes_basis
null
platform
null
taxon
null
title
SILAC labelled tendon fibroblasts
resolution_checked_at
2026-11-01T20:16:17Z
resolution_check
identifier_resolution_only_no_download_no_licence_read
downloaded
false
licence_read
false
gaps array · 2 items
[0]
asset:data:geo:PXD036794 not downloaded
[1]
asset:data:geo:PXD036794 licence not read
analysis object · 4 fields
state
partial
methods array · 2 items
[0] object · 10 fields
id
method-1
family
sequence_alignment
specific
blast
label
Sequence alignment / homology
dsl_operations array · 2 items
[0]
sequence_align
[1]
alignment_identity
missing_operations array · 0 items
parameters object · 0 fields
data_shapes array · 1 item
[0]
sequence_records
evidence object · 3 fields
score
0.8
band
high
quote
Blast
[1] object · 10 fields
id
method-2
family
null
specific
null
label
Student’s T-test, unpaired
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
** represents p<0.01, Student’s T-test, unpaired.
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 · 2 items
[0]
sequence_align
[1]
alignment_identity
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: blast.
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 · 1 item
[0]
PXD036794
resolved_accessions array · 1 item
[0]
PXD036794
statements array · 1 item
[0]
ProteomeXchange: Consortium via the PRIDE partner repository: mass spectrometry proteomics data. Accession number PXD036794; https://dx.doi.org/10.6019/PXD036794 ( Perez-Riverol et al., 2022).
basis
The paper names PXD036794 in ProteomeXchange Consortium via the PRIDE partner repository and the accession resolves in the repository. No dataset was downloaded and no licence was read.
can_run object · 3 fields
dsl_operations array · 2 items
[0]
sequence_align
[1]
alignment_identity
assets array · 2 items
[0]
source:pmid:41208827
[1]
data:geo:PXD036794
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:PXD036794
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
2026-11-01T20:05:07Z
independence
single_reader
evidence_check object · 2 fields
method
verbatim
availability
null
calls
5
usage object · 3 fields
prompt_tokens
17695
completion_tokens
1599
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:41208827
type
paper
label
pmid:41208827
[1] object · 3 fields
id
source:pmid:41208827
type
manuscript
label
PMID 41208827 full text
[2] object · 3 fields
id
data:geo:PXD036794
type
dataset
label
GEO PXD036794
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:41208827
type
paper
label
pmid:41208827
[1] object · 3 fields
id
source:pmid:41208827
type
manuscript
label
PMID 41208827 full text
[2] object · 3 fields
id
data:geo:PXD036794
type
dataset
label
GEO PXD036794
agent
agent:corpus-assay-engine
[1] object · 4 fields
id
activity-read-41208827
type
extraction
used array · 1 item
[0]
source:pmid:41208827
agent
agent:minimax-reader
[2] object · 4 fields
id
activity-resolve-PXD036794
type
accession_resolution
used array · 1 item
[0]
data:geo:PXD036794
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:41208827
parent_hash
sha256:047749f5da12ded95615f290fd818c538e093c468e1553628a2849797d7d5bb9
fork_of
null
gaps array · 7 items
[0]
asset:data:geo:PXD036794 licence not read
[1]
asset:data:geo:PXD036794 not downloaded
[2]
execution.not_run
[3]
method.reader_named_unmapped
[4]
review.human_critique
[5]
review.independent_reader
[6]
review.machine_critique
assays array · 5 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
0.99
evidence array · 3 items
[0]
of assembly is unclear. Methods: Here, using CRISPR-tagging of type I collagen, high-resolution
[1]
e seeded in 6 well plates overnight and then transfected with 100 pmol siRNAusing RNAiMAX. Protein, R
[2]
4.5 mm, 10 measurements per data point). For siRNA treatments, 200,000 cells were seeded in 6 w
order_basis
paper_text_order:202
id
assay:1
[1] object · 11 fields
role
data_generation
definition_id
mass_spectrometry
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]
ss and its regulation of health and disease. Mass spectrometry data were available via ProteomeXchange with
[1]
icated concentrations and immediately mixed. Proteomic sample preparation Cell pellets were resuspe
[2]
re digested with 0.8 µg/µL trypsin solution (Proteomics grade trypsin, Promega). The peptides were t
order_basis
paper_text_order:1087
id
assay:2
[2] 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
0.93
evidence array · 2 items
[0]
Research Ethical Committee, UK. Immortalized mouse embryonic fibroblasts, NIH3T3, were maintain
[1]
bovine serum, penicillin, and streptomycin. Mouse tendon fibroblasts were cultured in DMEM:F-1
order_basis
paper_text_order:1374
id
assay:3
[3] 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]
at µ-Dish (Ibidi, Germany). NIH3T3 and MC3T3 cell lines were cultured with 20 and 200 µg/mL l-ascorbic acid, respe
[1]
streptomycin. Mouse tendon fibroblasts were cultured in DMEM:F-12 (1:1) medium supplemented with 5%
[2]
, Germany). NIH3T3 and MC3T3 cell lines were cultured with 20 and 200 µg/mL l-ascorbic acid, respective
[3]
K. Immortalized mouse embryonic fibroblasts, NIH3T3, were maintained in DMEM supplemented with 1
order_basis
paper_text_order:1403
id
assay:4
[4] object · 11 fields
role
analysis
definition_id
sequence_alignment
definition_version
f2132e96ae6c7a4e
required_operations array · 2 items
[0]
sequence_align
[1]
alignment_identity
support_state
supported
source_hashes object · 1 field
dsl_catalogue
f2132e96ae6c7a4e
evidence array · 1 item
[0]
Blast
order_basis
consumes_earlier_output
id
assay:5
Complete file
{"sci_version": "1.2", "schema": "https://corpus.bntrg.co.uk/sci/1.0/sci.schema.json", "id": "pmid:41208827", "kind": "science-record", "revision": 3, "content_hash": "sha256:411a34088f7cbf6ce430645d8a6e47c6a499c2e645135ebf6e10381728a4fe30", "created_at": "2026-11-01T20:31:14Z", "updated_at": "2026-11-01T22:14:57Z", "generator": {"name": "corpus-assay-engine", "run_id": "reading-sci-2026-11-01"}, "paper": {"state": "complete", "title": "Collagen fibril formation at the plasma membrane occurs independently from collagen secretion.", "doi": "10.12688/wellcomeopenres.23776.1", "pmid": "41208827", "authors": ["Adam Pickard", "Richa Garva", "Antony Adamson", "Ben C Calverley", "Anna Hoyle", "Christina E Hayward", "David Spiller", "Yinhui Lu", "Nigel Hodson", "Oriana Mandolfo", "Kevin Kim", "George Bou-Gharios", "Joe Swift", "Brian Bigger", "Karl E Kadler"], "journal": "Wellcome open research", "year": 2025, "abstract": "Background: Collagen fibrils are the primary supporting scaffolds of vertebrate tissues, but the mechanism of assembly is unclear.\nMethods: Here, using CRISPR-tagging of type I collagen, high-resolution light imaging, and SILAC labelling, we elucidated the cellular mechanism underlying the spatiotemporal assembly of collagen fibrils in cultured fibroblasts.\nResults: Our findings reveal the multifaceted trafficking of collagen, including constitutive secretion, intracellular pooling, and plasma membrane-directed fibrillogenesis. Notably, we differentiated the processes of collagen secretion and fibril assembly and identified the crucial involvement of endocytosis in the regulation of fibril formation. By employing Col1a1 knockout fibroblasts, we demonstrated the incorporation of exogenous collagen into the nucleation sites at the plasma membrane through these recycling mechanisms.\nConclusions: Our study sheds light on a complex and previously unidentified collagen assembly process and its regulation of health and disease. Mass spectrometry data were available via ProteomeXchange with the identifier PXD036794.", "claims": [{"id": "claim-method", "statement": "** represents p<0.01, Student’s T-test, unpaired.", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:41208827", "locator": "sections[23] \"Collagen fibril formation blocked in the presence of monensin but not brefeldin A\" paragraph 3", "quote": "** represents p<0.01, Student’s T-test, unpaired."}], "state": "complete"}, {"id": "claim-data-access", "statement": "ProteomeXchange: Consortium via the PRIDE partner repository: mass spectrometry proteomics data. Accession number PXD036794; https://dx.doi.org/10.6019/PXD036794 ( Perez-Riverol et al., 2022).", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:41208827", "locator": "sections[29] \"Underlying data\" paragraph 2", "quote": "ProteomeXchange: Consortium via the PRIDE partner repository: mass spectrometry proteomics data. Accession number PXD036794; https://dx.doi.org/10.6019/PXD036794 ( Perez-Riverol et al., 2022)."}], "state": "complete"}], "gaps": []}, "experiment": {"state": "complete", "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:41208827"], "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:PXD036794"], "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:PXD036794"], "outputs": ["the replicated result and its comparison"], "instruments": [], "reagents": []}], "materials": [], "instruments": [], "reagents": [], "conditions": {}, "gaps": []}, "data": {"state": "partial", "assets": [{"id": "source:pmid:41208827", "role": "manuscript", "format": "xml", "media_type": "application/xml", "uri": "https://doi.org/10.12688/wellcomeopenres.23776.1", "sha256": "sha256:68c6a532a62b20e5765e255dacee560ded1df850cb44a6318c245e15f5ffe93b", "bytes": 66899, "access": "open", "state": "resolved", "reader": null, "reader_status": "reader_required", "identifier": "10.12688/wellcomeopenres.23776.1", "version": null, "note": "Full article fetched from PMC; the checksum covers the rendered section body, not the original XML bytes.", "structure": {"pmcid": "PMC12595305", "source": "europe_pmc_fulltext", "coverage": "whole_body_without_references", "text_hash_scope": "rendered_section_body"}}, {"id": "data:geo:PXD036794", "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=PXD036794", "sha256": null, "bytes": null, "access": "open", "state": "resolved", "reader": null, "reader_status": "reader_required", "identifier": "PXD036794", "version": null, "note": "ProteomeXchange: Consortium via the PRIDE partner repository: mass spectrometry proteomics data. Accession number PXD036794; https://dx.doi.org/10.6019/PXD036794 ( Perez-Riverol et al., 2022).", "structure": {"repository": "GEO", "access_route": "GEO accession URL", "access_statement_verbatim": "ProteomeXchange: Consortium via the PRIDE partner repository: mass spectrometry proteomics data. Accession number PXD036794; https://dx.doi.org/10.6019/PXD036794 ( Perez-Riverol et al., 2022).", "access_statement_kind": "repository_route_statement", "sample_accessions": [], "sample_count": null, "group_sizes": null, "group_sizes_basis": null, "platform": null, "taxon": null, "title": "SILAC labelled tendon fibroblasts", "resolution_checked_at": "2026-11-01T20:16:17Z", "resolution_check": "identifier_resolution_only_no_download_no_licence_read", "downloaded": false, "licence_read": false}}], "gaps": ["asset:data:geo:PXD036794 not downloaded", "asset:data:geo:PXD036794 licence not read"]}, "analysis": {"state": "partial", "methods": [{"id": "method-1", "family": "sequence_alignment", "specific": "blast", "label": "Sequence alignment / homology", "dsl_operations": ["sequence_align", "alignment_identity"], "missing_operations": [], "expressible": true, "parameters": {}, "data_shapes": ["sequence_records"], "evidence": {"score": 0.8, "band": "high", "quote": "Blast"}}, {"id": "method-2", "family": null, "specific": null, "label": "Student’s T-test, unpaired", "dsl_operations": [], "missing_operations": [], "expressible": null, "parameters": {}, "data_shapes": [], "evidence": {"score": 1.0, "band": "verbatim", "quote": "** represents p<0.01, Student’s T-test, unpaired."}}], "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": ["sequence_align", "alignment_identity"], "missing_operations": [], "basis": "The paper names the method it used and the corpus's method extractor maps it onto the DSL catalogue: blast."}, "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": ["PXD036794"], "resolved_accessions": ["PXD036794"], "statements": ["ProteomeXchange: Consortium via the PRIDE partner repository: mass spectrometry proteomics data. Accession number PXD036794; https://dx.doi.org/10.6019/PXD036794 ( Perez-Riverol et al., 2022)."], "basis": "The paper names PXD036794 in ProteomeXchange Consortium via the PRIDE partner repository and the accession resolves in the repository. No dataset was downloaded and no licence was read."}}, "can_run": {"dsl_operations": ["sequence_align", "alignment_identity"], "assets": ["source:pmid:41208827", "data:geo:PXD036794"], "steps": ["run_analysis"]}, "must_build": {"dsl_operations": [], "converters": [], "readers": [], "capabilities": [], "data_gaps": ["data:geo:PXD036794"]}, "gaps": []}, "review": {"state": "partial", "machine_critique": {"kind": "extraction_review", "reader": {"model": "MiniMax-M3.1-Flash", "provider": "minimax", "provider_family": "minimax", "read_at": "2026-11-01T20:05:07Z", "independence": "single_reader"}, "evidence_check": {"method": "verbatim", "availability": null}, "calls": 5, "usage": {"prompt_tokens": 17695, "completion_tokens": 1599, "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:41208827", "type": "paper", "label": "pmid:41208827"}, {"id": "source:pmid:41208827", "type": "manuscript", "label": "PMID 41208827 full text"}, {"id": "data:geo:PXD036794", "type": "dataset", "label": "GEO PXD036794"}], "activities": [{"id": "activity-reading-sci-2026-11-01", "type": "classification", "used": [{"id": "pmid:41208827", "type": "paper", "label": "pmid:41208827"}, {"id": "source:pmid:41208827", "type": "manuscript", "label": "PMID 41208827 full text"}, {"id": "data:geo:PXD036794", "type": "dataset", "label": "GEO PXD036794"}], "agent": "agent:corpus-assay-engine"}, {"id": "activity-read-41208827", "type": "extraction", "used": ["source:pmid:41208827"], "agent": "agent:minimax-reader"}, {"id": "activity-resolve-PXD036794", "type": "accession_resolution", "used": ["data:geo:PXD036794"], "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:41208827", "parent_hash": "sha256:047749f5da12ded95615f290fd818c538e093c468e1553628a2849797d7d5bb9", "fork_of": null, "generation": 2}, "gaps": ["asset:data:geo:PXD036794 licence not read", "asset:data:geo:PXD036794 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": 0.99, "evidence": ["of assembly is unclear. Methods: Here, using CRISPR-tagging of type I collagen, high-resolution", "e seeded in 6 well plates overnight and then transfected with 100 pmol siRNAusing RNAiMAX. Protein, R", "4.5 mm, 10 measurements per data point). For siRNA treatments, 200,000 cells were seeded in 6 w"], "order_basis": "paper_text_order:202", "id": "assay:1"}, {"role": "data_generation", "definition_id": "mass_spectrometry", "definition_version": "99e1195c7d6f", "definition_digest": null, "required_operations": [], "support_state": "partial", "source_hashes": {"assay_lexicon": "99e1195c7d6f"}, "confidence": 0.99, "evidence": ["ss and its regulation of health and disease. Mass spectrometry data were available via ProteomeXchange with", "icated concentrations and immediately mixed. Proteomic sample preparation Cell pellets were resuspe", "re digested with 0.8 µg/µL trypsin solution (Proteomics grade trypsin, Promega). The peptides were t"], "order_basis": "paper_text_order:1087", "id": "assay:2"}, {"role": "data_generation", "definition_id": "animal_model", "definition_version": "99e1195c7d6f", "definition_digest": null, "required_operations": [], "support_state": "partial", "source_hashes": {"assay_lexicon": "99e1195c7d6f"}, "confidence": 0.93, "evidence": ["Research Ethical Committee, UK. Immortalized mouse embryonic fibroblasts, NIH3T3, were maintain", "bovine serum, penicillin, and streptomycin. Mouse tendon fibroblasts were cultured in DMEM:F-1"], "order_basis": "paper_text_order:1374", "id": "assay:3"}, {"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": ["at µ-Dish (Ibidi, Germany). NIH3T3 and MC3T3 cell lines were cultured with 20 and 200 µg/mL l-ascorbic acid, respe", "streptomycin. Mouse tendon fibroblasts were cultured in DMEM:F-12 (1:1) medium supplemented with 5%", ", Germany). NIH3T3 and MC3T3 cell lines were cultured with 20 and 200 µg/mL l-ascorbic acid, respective", "K. Immortalized mouse embryonic fibroblasts, NIH3T3, were maintained in DMEM supplemented with 1"], "order_basis": "paper_text_order:1403", "id": "assay:4"}, {"role": "analysis", "definition_id": "sequence_alignment", "definition_version": "f2132e96ae6c7a4e", "definition_digest": null, "required_operations": ["sequence_align", "alignment_identity"], "support_state": "supported", "source_hashes": {"dsl_catalogue": "f2132e96ae6c7a4e"}, "confidence": 0.8, "evidence": ["Blast"], "order_basis": "consumes_earlier_output", "id": "assay:5"}]}