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

pmid:27077091

Whole transcriptome data analysis of mouse embryonic hematopoietic stem and progenitor cells that lack Geminin expression.

Alexandra L Patmanidi · Nikolaos I Kanellakis · Dimitris Karamitros · Christos Papadimitriou · Zoi Lygerou · Stavros Taraviras

Data in brief · 2016 doi:10.1016/j.dib.2016.03.028

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:27077091
kind
science-record
content_hash
sha256:e386e92f54855ca310d48995c29839df1110d531edf32817a98c650998e2cedb
schema
https://corpus.bntrg.co.uk/sci/1.0/sci.schema.json
created_at
2026-11-01T15:40:17Z
updated_at
2026-11-01T21:20:31Z
generator object · 2 fields
name
corpus-assay-engine
run_id
reading-sci-2026-11-01
paper object · 10 fields
state
complete
title
Whole transcriptome data analysis of mouse embryonic hematopoietic stem and progenitor cells that lack Geminin expression.
doi
10.1016/j.dib.2016.03.028
pmid
27077091
authors array · 6 items
[0]
Alexandra L Patmanidi
[1]
Nikolaos I Kanellakis
[2]
Dimitris Karamitros
[3]
Christos Papadimitriou
[4]
Zoi Lygerou
[5]
Stavros Taraviras
journal
Data in brief
year
2016
abstract
We performed cDNA microarrays (Affymetrix Mouse Gene 1.0 ST Chip) to analyze the transcriptome of hematopoietic stem and progenitor cells (HSPCs) from E15.5dpc wild type and Geminin (Gmnn) knockout embryos. Lineage negative cells from embryonic livers were isolated using fluorescence activated cell sorting. RNA samples were used to examine the transcriptional programs regulated by Geminin during embryonic hematopoiesis. The data sets were analyzed using the GeneSpring v12.5 platform (Agilent). The list of differentially expressed genes was filtered in meta-analyses to investigate the molecular basis of the phenotype observed in the knockout embryos, which exhibited defective hematopoiesis and death. The data from this study are related to the research article "Geminin deletion increases the number of fetal hematopoietic stem cells by affecting the expression of key transcription factors" (Karamitros et al., 2015) [1]. The microarray dataset has been deposited at the Gene Expression Omnibus (GEO) under accession GEO: GSE53056.
claims array · 3 items
[0] object · 6 fields
id
claim-method
statement
Statistical significance was assessed using Student׳s T-test unpaired (two separate sets of independent and identically distributed samples) with a 95% confidence interval (P-value<0.05). The data within this article and is publicly available at the Gene Expression Omnibus (GEO) under accession GEO: GSE53056.
kind
methodological
target
null
evidence array · 2 items
[0] object · 3 fields
asset
source:pmid:27077091
locator
sections[8] "Microarray data analysis" paragraph 2
quote
Statistical significance was assessed using Student׳s T-test unpaired (two separate sets of independent and identically distributed samples) with a 95% confidence interval (P-value<0.05).
[1] object · 3 fields
asset
source:pmid:27077091
locator
sections[1] "p" paragraph 1
quote
The data within this article and is publicly available at the Gene Expression Omnibus (GEO) under accession GEO: GSE53056.
state
complete
[1] object · 6 fields
id
claim-data-access
statement
The data within this article and is publicly available at the Gene Expression Omnibus (GEO) under accession GEO: GSE53056.
kind
methodological
target
null
evidence array · 1 item
[0] object · 3 fields
asset
source:pmid:27077091
locator
sections[1] "p" paragraph 1
quote
The data within this article and is publicly available at the Gene Expression Omnibus (GEO) under accession GEO: GSE53056.
state
complete
[2] object · 6 fields
id
claim-target-result
statement
The paper reports that statistical significance was assessed using Student׳s T-test unpaired with a 95% confidence interval (P-value<0.05), using a fold-change cutoff greater than 1.5; the source data are publicly available at GEO under accession GSE53056.
kind
quantitative
target object · 4 fields
value
95
unit
per cent
tolerance
null
source
Statistical significance was assessed using Student׳s T-test unpaired (two separate sets of independent and identically distributed samples) with a 95% confidence interval (P-value<0.05).
evidence array · 4 items
[0] object · 3 fields
asset
source:pmid:27077091
locator
sections[0] "Abstract" paragraph 1
quote
The data sets were analyzed using the GeneSpring v12.5 platform (Agilent).
[1] object · 3 fields
asset
source:pmid:27077091
locator
sections[0] "Abstract" paragraph 2
quote
The microarray dataset has been deposited at the Gene Expression Omnibus (GEO) under accession GEO: GSE53056.
[2] object · 3 fields
asset
source:pmid:27077091
locator
sections[8] "Microarray data analysis" paragraph 2
quote
Statistical significance was assessed using Student׳s T-test unpaired (two separate sets of independent and identically distributed samples) with a 95% confidence interval (P-value<0.05).
[3] object · 3 fields
asset
source:pmid:27077091
locator
sections[8] "Microarray data analysis" paragraph 2
quote
The cutoff value for the fold change of the genes was set to be greater than 1.5.
state
complete
gaps array · 0 items
experiment object · 8 fields
state
partial
objective
The paper reports that statistical significance was assessed using Student׳s T-test unpaired with a 95% confidence interval (P-value<0.05), using a fold-change cutoff greater than 1.5; the source data are publicly available at GEO under accession GSE53056.
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:27077091
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
blocked
blocked_on
data:accession_absent
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 · 0 items
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 · 0 items
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:obtain_source_data blocked on data:accession_absent
data object · 3 fields
state
partial
assets array · 3 items
[0] object · 15 fields
id
source:pmid:27077091
role
manuscript
format
xml
media_type
application/xml
uri
https://doi.org/10.1016/j.dib.2016.03.028
sha256
sha256:6656edb4f151eddbaebdb0f241e2df340fade9eb5fdc76cca38be6a190ccf969
bytes
6268
access
open
state
resolved
reader
null
reader_status
reader_required
identifier
10.1016/j.dib.2016.03.028
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
PMC4816909
source
europe_pmc_fulltext
coverage
whole_body_without_references
text_hash_scope
rendered_section_body
[1] object · 16 fields
id
asset:table:pmid:27077091:1
role
table
format
jats-table
media_type
application/vnd.jats.table+json
uri
null
sha256
sha256:43d719e094b645953d6e69122560ee9b103495f24a090a34da00c6379be18001
bytes
1204
access
open
state
verified
reader
read_table
reader_status
available
identifier
section[1]/table-wrap[1]#t0010
version
null
note
null
structure object · 5 fields
pmcid
PMC4816909
section_index
1
section_title
p
row_count
8
column_count
2
table object · 8 fields
label
null
caption
null
rows array · 8 items
[0] array · 2 items
[0]
Subject area
[1]
Biology
[1] array · 2 items
[0]
More specific subject area
[1]
Developmental/Stem cell biology
[2] array · 2 items
[0]
Type of data
[1]
Figure (clustering), graph, table
[3] array · 2 items
[0]
How data was acquired
[1]
cDNA microarrays using GPL6246 [MoGene-1_0-st] Affymetrix Mouse Gene 1.0 ST Array [transcript (gene) version]. Organism: Mus Musculus. Strain background: C57BL6. Developmental stage: E15.5. Tissue: Fetal liver. Cell type: Lineage negative embryonic hematopoietic cells, Genotype: Gemininwt/wt or Geminin fl/wt (control) [2] and Gemininfl/ko Vav1:iCre [2, 3] (knock out) mouse lines
[4] array · 2 items
[0]
Data format
[1]
Analyzed using Genespring v12.5
[5] array · 2 items
[0]
Experimental features
[1]
Wild type and embryos lacking Geminin from the hematopoietic stem and progenitor cells (HSPCs); RNA from HSPCs; HSCPs were isolated using FACS sorting from dissected fetal livers
[6] array · 2 items
[0]
Data source location
[1]
Department of Physiology, Medical School, University of Patras, Greece
[7] array · 2 items
[0]
Data accessibility
[1]
The data within this article and is publicly available at the Gene Expression Omnibus (GEO) under accession GEO: GSE53056.
locator
section[1]/table-wrap[1]#t0010
[2] object · 16 fields
id
asset:table:pmid:27077091:2
role
table
format
jats-table
media_type
application/vnd.jats.table+json
uri
null
sha256
sha256:43d719e094b645953d6e69122560ee9b103495f24a090a34da00c6379be18001
bytes
1204
access
open
state
verified
reader
read_table
reader_status
available
identifier
section[1]/table-wrap[1]#t0010
version
null
note
null
structure object · 5 fields
pmcid
PMC4816909
section_index
2
section_title
p
row_count
8
column_count
2
table object · 8 fields
label
null
caption
null
rows array · 8 items
[0] array · 2 items
[0]
Subject area
[1]
Biology
[1] array · 2 items
[0]
More specific subject area
[1]
Developmental/Stem cell biology
[2] array · 2 items
[0]
Type of data
[1]
Figure (clustering), graph, table
[3] array · 2 items
[0]
How data was acquired
[1]
cDNA microarrays using GPL6246 [MoGene-1_0-st] Affymetrix Mouse Gene 1.0 ST Array [transcript (gene) version]. Organism: Mus Musculus. Strain background: C57BL6. Developmental stage: E15.5. Tissue: Fetal liver. Cell type: Lineage negative embryonic hematopoietic cells, Genotype: Gemininwt/wt or Geminin fl/wt (control) [2] and Gemininfl/ko Vav1:iCre [2, 3] (knock out) mouse lines
[4] array · 2 items
[0]
Data format
[1]
Analyzed using Genespring v12.5
[5] array · 2 items
[0]
Experimental features
[1]
Wild type and embryos lacking Geminin from the hematopoietic stem and progenitor cells (HSPCs); RNA from HSPCs; HSCPs were isolated using FACS sorting from dissected fetal livers
[6] array · 2 items
[0]
Data source location
[1]
Department of Physiology, Medical School, University of Patras, Greece
[7] array · 2 items
[0]
Data accessibility
[1]
The data within this article and is publicly available at the Gene Expression Omnibus (GEO) under accession GEO: GSE53056.
locator
section[1]/table-wrap[1]#t0010
gaps array · 0 items
analysis object · 4 fields
state
partial
methods array · 1 item
[0] object · 10 fields
id
method-1
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
reordered
quote
Statistical significance was assessed using Student׳s T-test unpaired (two separate sets of independent and identically distributed samples) with a 95% confidence interval (P-value<0.05). The data within this article and is publicly available at the Gene Expression Omnibus (GEO) under accession GEO: GSE53056.
targets array · 2 items
[0] object · 8 fields
id
target-published-estimate
claim_id
claim-target-result
operation
null
unit
per cent
tolerance
null
state
complete
note
The published estimate as the reader quoted it from the paper. No tolerance is published because the paper states none.
[1] object · 8 fields
id
target-published-estimate-p-value
claim_id
claim-target-result
operation
null
unit
p-value
tolerance
null
state
complete
note
The threshold the paper applied to its own result, as the paper states it. A run that reproduces the effect is judged against this threshold.
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
blocked
tier
R4
blocked_on
data:accession_absent
axes object · 3 fields
method object · 5 fields
tier
R4
expressible
false
required_operations array · 0 items
missing_operations array · 0 items
basis
The reader quoted the method the paper names (Student’s T-test, unpaired), but the corpus's method extractor could not map it onto a DSL operation, so the method is published but not expressible.
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
R4
reachable
false
accessions array · 1 item
[0]
GEO: GSE53056
resolved_accessions array · 0 items
statements array · 1 item
[0]
The data within this article and is publicly available at the Gene Expression Omnibus (GEO) under accession GEO: GSE53056.
basis
The paper names GEO: GSE53056, but the accession does not resolve in the repository (no reason recorded), so the data cannot be reached from here. No dataset was downloaded and no licence was read.
can_run object · 3 fields
dsl_operations array · 0 items
assets array · 3 items
[0]
source:pmid:27077091
[1]
asset:table:pmid:27077091:1
[2]
asset:table:pmid:27077091:2
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:None
gaps array · 1 item
[0]
data:accession_absent
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
2026-10-31T18:28:10Z
independence
same_provider
evidence_check object · 2 fields
method
reordered
availability
verbatim
calls
8
usage object · 3 fields
prompt_tokens
16542
completion_tokens
3211
cached_tokens
1416
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:27077091
type
paper
label
pmid:27077091
[1] object · 3 fields
id
source:pmid:27077091
type
manuscript
label
PMID 27077091 full text
[2] object · 3 fields
id
data:geo:None
type
dataset
label
GEO None
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:27077091
type
paper
label
pmid:27077091
[1] object · 3 fields
id
source:pmid:27077091
type
manuscript
label
PMID 27077091 full text
[2] object · 3 fields
id
data:geo:None
type
dataset
label
GEO None
agent
agent:corpus-assay-engine
[1] object · 4 fields
id
activity-read-27077091
type
extraction
used array · 1 item
[0]
source:pmid:27077091
agent
agent:minimax-reader
[2] object · 4 fields
id
activity-resolve-None
type
accession_resolution
used array · 1 item
[0]
data:geo:None
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:27077091
parent_hash
sha256:4f4c1e11de0cfe72132ca3cd764e3d50e2733b86a2727029c240089cecd22a21
fork_of
null
gaps array · 6 items
[0]
execution.not_run
[1]
method.reader_named_unmapped
[2]
review.human_critique
[3]
review.independent_reader
[4]
review.machine_critique
[5]
step:obtain_source_data blocked on data:accession_absent
assays array · 3 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
0.93
evidence array · 2 items
[0]
Whole transcriptome data analysis of mouse embryonic hematopoietic stem and progenitor
[1]
We performed cDNA microarrays (Affymetrix Mouse Gene 1.0 ST Chip) to analyze the transcripto
order_basis
paper_text_order:0
id
assay:1
[1] object · 11 fields
role
data_generation
definition_id
microarray
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]
factors" (Karamitros et al., 2015) [1]. The microarray dataset has been deposited at the Gene Expre
[1]
We performed cDNA microarrays (Affymetrix Mouse Gene 1.0 ST Chip) to analyze the trans
order_basis
paper_text_order:123
id
assay:2
[2] object · 11 fields
role
data_generation
definition_id
flow_cytometry
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]
ls from embryonic livers were isolated using fluorescence activated cell sorting. RNA samples were used to examine the transc
[1]
s were isolated using fluorescence activated cell sorting. RNA samples were used to examine the transc
[2]
l livers from E15.5 embryos were isolated by FACS sorting with known blood cell lineage marker
order_basis
paper_text_order:350
id
assay:3
Complete file
{"sci_version": "1.2", "schema": "https://corpus.bntrg.co.uk/sci/1.0/sci.schema.json", "id": "pmid:27077091", "kind": "science-record", "revision": 6, "content_hash": "sha256:e386e92f54855ca310d48995c29839df1110d531edf32817a98c650998e2cedb", "created_at": "2026-11-01T15:40:17Z", "updated_at": "2026-11-01T21:20:31Z", "generator": {"name": "corpus-assay-engine", "run_id": "reading-sci-2026-11-01"}, "paper": {"state": "complete", "title": "Whole transcriptome data analysis of mouse embryonic hematopoietic stem and progenitor cells that lack Geminin expression.", "doi": "10.1016/j.dib.2016.03.028", "pmid": "27077091", "authors": ["Alexandra L Patmanidi", "Nikolaos I Kanellakis", "Dimitris Karamitros", "Christos Papadimitriou", "Zoi Lygerou", "Stavros Taraviras"], "journal": "Data in brief", "year": 2016, "abstract": "We performed cDNA microarrays (Affymetrix Mouse Gene 1.0 ST Chip) to analyze the transcriptome of hematopoietic stem and progenitor cells (HSPCs) from E15.5dpc wild type and Geminin (Gmnn) knockout embryos. Lineage negative cells from embryonic livers were isolated using fluorescence activated cell sorting. RNA samples were used to examine the transcriptional programs regulated by Geminin during embryonic hematopoiesis. The data sets were analyzed using the GeneSpring v12.5 platform (Agilent). The list of differentially expressed genes was filtered in meta-analyses to investigate the molecular basis of the phenotype observed in the knockout embryos, which exhibited defective hematopoiesis and death. The data from this study are related to the research article \"Geminin deletion increases the number of fetal hematopoietic stem cells by affecting the expression of key transcription factors\" (Karamitros et al., 2015) [1]. The microarray dataset has been deposited at the Gene Expression Omnibus (GEO) under accession GEO: GSE53056.", "claims": [{"id": "claim-method", "statement": "Statistical significance was assessed using Student׳s T-test unpaired (two separate sets of independent and identically distributed samples) with a 95% confidence interval (P-value<0.05). The data within this article and is publicly available at the Gene Expression Omnibus (GEO) under accession GEO: GSE53056.", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:27077091", "locator": "sections[8] \"Microarray data analysis\" paragraph 2", "quote": "Statistical significance was assessed using Student׳s T-test unpaired (two separate sets of independent and identically distributed samples) with a 95% confidence interval (P-value<0.05)."}, {"asset": "source:pmid:27077091", "locator": "sections[1] \"p\" paragraph 1", "quote": "The data within this article and is publicly available at the Gene Expression Omnibus (GEO) under accession GEO: GSE53056."}], "state": "complete"}, {"id": "claim-data-access", "statement": "The data within this article and is publicly available at the Gene Expression Omnibus (GEO) under accession GEO: GSE53056.", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:27077091", "locator": "sections[1] \"p\" paragraph 1", "quote": "The data within this article and is publicly available at the Gene Expression Omnibus (GEO) under accession GEO: GSE53056."}], "state": "complete"}, {"id": "claim-target-result", "statement": "The paper reports that statistical significance was assessed using Student׳s T-test unpaired with a 95% confidence interval (P-value<0.05), using a fold-change cutoff greater than 1.5; the source data are publicly available at GEO under accession GSE53056.", "kind": "quantitative", "target": {"value": 95.0, "unit": "per cent", "tolerance": null, "source": "Statistical significance was assessed using Student׳s T-test unpaired (two separate sets of independent and identically distributed samples) with a 95% confidence interval (P-value<0.05)."}, "evidence": [{"asset": "source:pmid:27077091", "locator": "sections[0] \"Abstract\" paragraph 1", "quote": "The data sets were analyzed using the GeneSpring v12.5 platform (Agilent)."}, {"asset": "source:pmid:27077091", "locator": "sections[0] \"Abstract\" paragraph 2", "quote": "The microarray dataset has been deposited at the Gene Expression Omnibus (GEO) under accession GEO: GSE53056."}, {"asset": "source:pmid:27077091", "locator": "sections[8] \"Microarray data analysis\" paragraph 2", "quote": "Statistical significance was assessed using Student׳s T-test unpaired (two separate sets of independent and identically distributed samples) with a 95% confidence interval (P-value<0.05)."}, {"asset": "source:pmid:27077091", "locator": "sections[8] \"Microarray data analysis\" paragraph 2", "quote": "The cutoff value for the fold change of the genes was set to be greater than 1.5."}], "state": "complete"}], "gaps": []}, "experiment": {"state": "partial", "objective": "The paper reports that statistical significance was assessed using Student׳s T-test unpaired with a 95% confidence interval (P-value<0.05), using a fold-change cutoff greater than 1.5; the source data are publicly available at GEO under accession GSE53056.", "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:27077091"], "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": "blocked", "blocked_on": "data:accession_absent", "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": [], "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": [], "outputs": ["the replicated result and its comparison"], "instruments": [], "reagents": []}], "materials": [], "instruments": [], "reagents": [], "conditions": {}, "gaps": ["step:obtain_source_data blocked on data:accession_absent"]}, "data": {"state": "partial", "assets": [{"id": "source:pmid:27077091", "role": "manuscript", "format": "xml", "media_type": "application/xml", "uri": "https://doi.org/10.1016/j.dib.2016.03.028", "sha256": "sha256:6656edb4f151eddbaebdb0f241e2df340fade9eb5fdc76cca38be6a190ccf969", "bytes": 6268, "access": "open", "state": "resolved", "reader": null, "reader_status": "reader_required", "identifier": "10.1016/j.dib.2016.03.028", "version": null, "note": "Full article fetched from PMC; the checksum covers the rendered section body, not the original XML bytes.", "structure": {"pmcid": "PMC4816909", "source": "europe_pmc_fulltext", "coverage": "whole_body_without_references", "text_hash_scope": "rendered_section_body"}}, {"id": "asset:table:pmid:27077091:1", "role": "table", "format": "jats-table", "media_type": "application/vnd.jats.table+json", "uri": null, "sha256": "sha256:43d719e094b645953d6e69122560ee9b103495f24a090a34da00c6379be18001", "bytes": 1204, "access": "open", "state": "verified", "reader": "read_table", "reader_status": "available", "identifier": "section[1]/table-wrap[1]#t0010", "version": null, "note": null, "structure": {"pmcid": "PMC4816909", "section_index": 1, "section_title": "p", "row_count": 8, "column_count": 2}, "table": {"label": null, "caption": null, "rows": [["Subject area", "Biology"], ["More specific subject area", "Developmental/Stem cell biology"], ["Type of data", "Figure (clustering), graph, table"], ["How data was acquired", "cDNA microarrays using GPL6246 [MoGene-1_0-st] Affymetrix Mouse Gene 1.0 ST Array [transcript (gene) version]. Organism: Mus Musculus. Strain background: C57BL6. Developmental stage: E15.5. Tissue: Fetal liver. Cell type: Lineage negative embryonic hematopoietic cells, Genotype: Gemininwt/wt or Geminin fl/wt (control) [2] and Gemininfl/ko Vav1:iCre [2, 3] (knock out) mouse lines"], ["Data format", "Analyzed using Genespring v12.5"], ["Experimental features", "Wild type and embryos lacking Geminin from the hematopoietic stem and progenitor cells (HSPCs); RNA from HSPCs; HSCPs were isolated using FACS sorting from dissected fetal livers"], ["Data source location", "Department of Physiology, Medical School, University of Patras, Greece"], ["Data accessibility", "The data within this article and is publicly available at the Gene Expression Omnibus (GEO) under accession GEO: GSE53056."]], "row_count": 8, "column_count": 2, "numeric_cells": 3, "header_rows": 0, "locator": "section[1]/table-wrap[1]#t0010"}}, {"id": "asset:table:pmid:27077091:2", "role": "table", "format": "jats-table", "media_type": "application/vnd.jats.table+json", "uri": null, "sha256": "sha256:43d719e094b645953d6e69122560ee9b103495f24a090a34da00c6379be18001", "bytes": 1204, "access": "open", "state": "verified", "reader": "read_table", "reader_status": "available", "identifier": "section[1]/table-wrap[1]#t0010", "version": null, "note": null, "structure": {"pmcid": "PMC4816909", "section_index": 2, "section_title": "p", "row_count": 8, "column_count": 2}, "table": {"label": null, "caption": null, "rows": [["Subject area", "Biology"], ["More specific subject area", "Developmental/Stem cell biology"], ["Type of data", "Figure (clustering), graph, table"], ["How data was acquired", "cDNA microarrays using GPL6246 [MoGene-1_0-st] Affymetrix Mouse Gene 1.0 ST Array [transcript (gene) version]. Organism: Mus Musculus. Strain background: C57BL6. Developmental stage: E15.5. Tissue: Fetal liver. Cell type: Lineage negative embryonic hematopoietic cells, Genotype: Gemininwt/wt or Geminin fl/wt (control) [2] and Gemininfl/ko Vav1:iCre [2, 3] (knock out) mouse lines"], ["Data format", "Analyzed using Genespring v12.5"], ["Experimental features", "Wild type and embryos lacking Geminin from the hematopoietic stem and progenitor cells (HSPCs); RNA from HSPCs; HSCPs were isolated using FACS sorting from dissected fetal livers"], ["Data source location", "Department of Physiology, Medical School, University of Patras, Greece"], ["Data accessibility", "The data within this article and is publicly available at the Gene Expression Omnibus (GEO) under accession GEO: GSE53056."]], "row_count": 8, "column_count": 2, "numeric_cells": 3, "header_rows": 0, "locator": "section[1]/table-wrap[1]#t0010"}}], "gaps": []}, "analysis": {"state": "partial", "methods": [{"id": "method-1", "family": null, "specific": null, "label": "Student’s T-test, unpaired", "dsl_operations": [], "missing_operations": [], "expressible": null, "parameters": {}, "data_shapes": [], "evidence": {"score": 1.0, "band": "reordered", "quote": "Statistical significance was assessed using Student׳s T-test unpaired (two separate sets of independent and identically distributed samples) with a 95% confidence interval (P-value<0.05). The data within this article and is publicly available at the Gene Expression Omnibus (GEO) under accession GEO: GSE53056."}}], "targets": [{"id": "target-published-estimate", "claim_id": "claim-target-result", "operation": null, "expected_value": 95.0, "unit": "per cent", "tolerance": null, "state": "complete", "note": "The published estimate as the reader quoted it from the paper. No tolerance is published because the paper states none."}, {"id": "target-published-estimate-p-value", "claim_id": "claim-target-result", "operation": null, "expected_value": 0.05, "unit": "p-value", "tolerance": null, "state": "complete", "note": "The threshold the paper applied to its own result, as the paper states it. A run that reproduces the effect is judged against this threshold."}], "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": "blocked", "tier": "R4", "blocking_axis": "data", "blocked_on": "data:accession_absent", "axes": {"method": {"tier": "R4", "expressible": false, "required_operations": [], "missing_operations": [], "basis": "The reader quoted the method the paper names (Student’s T-test, unpaired), but the corpus's method extractor could not map it onto a DSL operation, so the method is published but not expressible."}, "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": "R4", "reachable": false, "accessions": ["GEO: GSE53056"], "resolved_accessions": [], "statements": ["The data within this article and is publicly available at the Gene Expression Omnibus (GEO) under accession GEO: GSE53056."], "basis": "The paper names GEO: GSE53056, but the accession does not resolve in the repository (no reason recorded), so the data cannot be reached from here. No dataset was downloaded and no licence was read."}}, "can_run": {"dsl_operations": [], "assets": ["source:pmid:27077091", "asset:table:pmid:27077091:1", "asset:table:pmid:27077091:2"], "steps": ["run_analysis"]}, "must_build": {"dsl_operations": [], "converters": [], "readers": [], "capabilities": [], "data_gaps": ["data:geo:None"]}, "gaps": ["data:accession_absent"]}, "review": {"state": "partial", "machine_critique": {"kind": "extraction_review", "reader": {"model": "MiniMax-M3.1-Flash", "provider": "minimax", "provider_family": "minimax", "read_at": "2026-10-31T18:28:10Z", "independence": "same_provider"}, "evidence_check": {"method": "reordered", "availability": "verbatim"}, "calls": 8, "usage": {"prompt_tokens": 16542, "completion_tokens": 3211, "cached_tokens": 1416}}, "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:27077091", "type": "paper", "label": "pmid:27077091"}, {"id": "source:pmid:27077091", "type": "manuscript", "label": "PMID 27077091 full text"}, {"id": "data:geo:None", "type": "dataset", "label": "GEO None"}], "activities": [{"id": "activity-reading-sci-2026-11-01", "type": "classification", "used": [{"id": "pmid:27077091", "type": "paper", "label": "pmid:27077091"}, {"id": "source:pmid:27077091", "type": "manuscript", "label": "PMID 27077091 full text"}, {"id": "data:geo:None", "type": "dataset", "label": "GEO None"}], "agent": "agent:corpus-assay-engine"}, {"id": "activity-read-27077091", "type": "extraction", "used": ["source:pmid:27077091"], "agent": "agent:minimax-reader"}, {"id": "activity-resolve-None", "type": "accession_resolution", "used": ["data:geo:None"], "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:27077091", "parent_hash": "sha256:4f4c1e11de0cfe72132ca3cd764e3d50e2733b86a2727029c240089cecd22a21", "fork_of": null, "generation": 5}, "gaps": ["execution.not_run", "method.reader_named_unmapped", "review.human_critique", "review.independent_reader", "review.machine_critique", "step:obtain_source_data blocked on data:accession_absent"], "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": 0.93, "evidence": ["Whole transcriptome data analysis of mouse embryonic hematopoietic stem and progenitor", "We performed cDNA microarrays (Affymetrix Mouse Gene 1.0 ST Chip) to analyze the transcripto"], "order_basis": "paper_text_order:0", "id": "assay:1"}, {"role": "data_generation", "definition_id": "microarray", "definition_version": "99e1195c7d6f", "definition_digest": null, "required_operations": [], "support_state": "partial", "source_hashes": {"assay_lexicon": "99e1195c7d6f"}, "confidence": 0.99, "evidence": ["factors\" (Karamitros et al., 2015) [1]. The microarray dataset has been deposited at the Gene Expre", "We performed cDNA microarrays (Affymetrix Mouse Gene 1.0 ST Chip) to analyze the trans"], "order_basis": "paper_text_order:123", "id": "assay:2"}, {"role": "data_generation", "definition_id": "flow_cytometry", "definition_version": "99e1195c7d6f", "definition_digest": null, "required_operations": [], "support_state": "partial", "source_hashes": {"assay_lexicon": "99e1195c7d6f"}, "confidence": 0.99, "evidence": ["ls from embryonic livers were isolated using fluorescence activated cell sorting. RNA samples were used to examine the transc", "s were isolated using fluorescence activated cell sorting. RNA samples were used to examine the transc", "l livers from E15.5 embryos were isolated by FACS sorting with known blood cell lineage marker"], "order_basis": "paper_text_order:350", "id": "assay:3"}]}