← All .science files
pmid:26484239
RNA-Seq analysis of isolated satellite cells in Prmt5 deficient mice.
Carsten Kuenne · Stefan Guenther · Mario Looso · Ting Zhang · Marcus Krueger · Yonggang Zhou · Thomas Braun · Johnny Kim
Genomics data · 2015 doi:10.1016/j.gdata.2015.05.013
Paper
complete
Experiment
complete
Data
partial
Analysis
complete
Execution
absent
Execution evidence has not yet been added to this .science file. Explore its methods, data and open questions to plan the next step.
Record details sci_version · id · kind · revision · content_hash · schema · created_at · updated_at · generator
paper object · 10 fields
authors array · 8 items
claims array · 3 items
[0] object · 6 fields
[1] object · 6 fields
[2] object · 6 fields
gaps array · 0 items
experiment object · 8 fields
steps array · 3 items
[0] object · 13 fields
parameters object · 0 fields
inputs array · 1 item
outputs array · 1 item
instruments array · 0 items
reagents array · 0 items
[1] object · 13 fields
parameters object · 0 fields
inputs array · 1 item
outputs array · 1 item
instruments array · 0 items
reagents array · 0 items
[2] object · 13 fields
parameters object · 0 fields
inputs array · 1 item
outputs array · 1 item
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
assets array · 3 items
[0] object · 15 fields
structure object · 4 fields
[1] object · 15 fields
structure object · 15 fields
sample_accessions array · 4 items
[2] object · 16 fields
structure object · 5 fields
table object · 8 fields
rows array · 8 items
[0] array · 1 item
[1] array · 2 items
[2] array · 2 items
[3] array · 2 items
[4] array · 2 items
[5] array · 2 items
[6] array · 2 items
[7] array · 2 items
gaps array · 2 items
analysis object · 4 fields
methods array · 1 item
[0] object · 10 fields
dsl_operations array · 3 items
missing_operations array · 0 items
parameters object · 0 fields
data_shapes array · 1 item
targets array · 0 items
gaps array · 0 items
capability object · 3 fields
requirements array · 1 item
[0] object · 6 fields
assay_families array · 9 items
gaps array · 0 items
readiness object · 8 fields
axes object · 3 fields
method object · 5 fields
required_operations array · 3 items
missing_operations array · 0 items
capability object · 4 fields
data object · 6 fields
accessions array · 1 item
resolved_accessions array · 1 item
statements array · 1 item
can_run object · 3 fields
dsl_operations array · 3 items
assets array · 3 items
steps array · 1 item
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
gaps array · 0 items
review object · 5 fields
machine_critique object · 5 fields
reader object · 5 fields
evidence_check object · 2 fields
usage object · 3 fields
stages array · 1 item
[0] object · 4 fields
gaps array · 3 items
provenance object · 7 fields
entities array · 3 items
activities array · 3 items
[0] object · 4 fields
used array · 3 items
[0] object · 3 fields
[1] object · 3 fields
[2] object · 3 fields
[1] object · 4 fields
agents array · 2 items
lineage object · 4 fields
gaps array · 6 items
assays array · 4 items
[0] object · 11 fields
required_operations array · 0 items
source_hashes object · 1 field
evidence array · 3 items
[1] object · 11 fields
required_operations array · 0 items
source_hashes object · 1 field
evidence array · 3 items
[2] object · 11 fields
required_operations array · 0 items
source_hashes object · 1 field
evidence array · 2 items
[3] object · 11 fields
required_operations array · 3 items
source_hashes object · 1 field
evidence array · 1 item
Complete file
{"sci_version": "1.2", "schema": "https://corpus.bntrg.co.uk/sci/1.0/sci.schema.json", "id": "pmid:26484239", "kind": "science-record", "revision": 8, "content_hash": "sha256:77a1c396748f4cadcb86c74019626da962d118a53bc8bc65cdd6c9205a329907", "created_at": "2026-11-01T15:40:12Z", "updated_at": "2026-11-01T22:42:24Z", "generator": {"name": "corpus-assay-engine", "run_id": "reading-sci-2026-11-01"}, "paper": {"state": "complete", "title": "RNA-Seq analysis of isolated satellite cells in Prmt5 deficient mice.", "doi": "10.1016/j.gdata.2015.05.013", "pmid": "26484239", "authors": ["Carsten Kuenne", "Stefan Guenther", "Mario Looso", "Ting Zhang", "Marcus Krueger", "Yonggang Zhou", "Thomas Braun", "Johnny Kim"], "journal": "Genomics data", "year": 2015, "abstract": "Satellite cells (SCs) represent a distinct population of stem cells, essential for maintenance, growth and regeneration of adult skeletal muscle. SCs are mononuclear and are located between the basal lamina and the plasma membrane of myofibers. They are typically characterized by presence of the transcription factor paired-box 7 (PAX7) that is widely used as a satellite cell marker. Under normal physiological conditions SCs are quiescent but are activated by insults such as injury, disease or exercise. Once activated, satellite cells proliferate and subsequently differentiate into myoblasts to finally fuse to form new myofibers or with preexisting myofibers to repair or rebuild the skeletal muscle. A minority of SCs retains stem cell characteristics and self-renews to assure future bouts of regeneration throughout most of adult life. While a comprehensive picture of the regulatory events controlling SC fate has not yet been achieved, several factors were recently identified playing important roles in functional processes. One example is the arginine methyltransferase Prmt5 that is known to have multiple roles in germ cells and is involved in the maintenance of ES cell pluripotency. We have previously shown that Prmt5 is required for muscle stem cell proliferation and regenerative myogenesis due to direct epigenetic regulation of the cell cycle inhibitor p21. Here we provide a dataset that investigates the loss of Prmt5 in isolated Pax7(+) primary SCs using the Pax7(CreERT2)/Prmt5(loxP/loxP) knockout mouse model. RNA-Seq raw and analyzed data have been deposited in GEO under accession code GSE66822.", "claims": [{"id": "claim-method", "statement": "Differentially expressed genes were identified using DESeq2 version 1.62 [8].", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:26484239", "locator": "sections[7] \"Differential expression analyses\" paragraph 2", "quote": "Differentially expressed genes were identified using DESeq2 version 1.62 [8]."}], "state": "complete"}, {"id": "claim-data-access", "statement": "RNA-Seq raw and analyzed data have been deposited in GEO under accession code GSE66822.", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:26484239", "locator": "sections[0] \"Abstract\" paragraph 2", "quote": "RNA-Seq raw and analyzed data have been deposited in GEO under accession code GSE66822."}], "state": "complete"}, {"id": "claim-target-result", "statement": "The study identified differentially expressed genes using DESeq2 and deposited the raw and analyzed RNA-Seq data in GEO under accession code GSE66822.", "kind": "qualitative", "target": null, "evidence": [{"asset": "source:pmid:26484239", "locator": "sections[0] \"Abstract\" paragraph 1", "quote": "Here we provide a dataset that investigates the loss of Prmt5 in isolated Pax7+ primary SCs using the Pax7CreERT2/Prmt5loxP/loxP knockout mouse model."}, {"asset": "source:pmid:26484239", "locator": "sections[7] \"Differential expression analyses\" paragraph 2", "quote": "Differentially expressed genes were identified using DESeq2 version 1.62 [8]."}, {"asset": "source:pmid:26484239", "locator": "sections[0] \"Abstract\" paragraph 2", "quote": "RNA-Seq raw and analyzed data have been deposited in GEO under accession code GSE66822."}], "state": "complete"}], "gaps": []}, "experiment": {"state": "complete", "objective": "The study identified differentially expressed genes using DESeq2 and deposited the raw and analyzed RNA-Seq data in GEO under accession code GSE66822.", "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:26484239"], "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:GSE66822"], "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:GSE66822"], "outputs": ["the replicated result and its comparison"], "instruments": [], "reagents": []}], "materials": [], "instruments": [], "reagents": [], "conditions": {}, "gaps": []}, "data": {"state": "partial", "assets": [{"id": "source:pmid:26484239", "role": "manuscript", "format": "xml", "media_type": "application/xml", "uri": "https://doi.org/10.1016/j.gdata.2015.05.013", "sha256": "sha256:d08f2fb3608fbdae23824e38495cad442027b58f87934966a89070667bd3b772", "bytes": 6790, "access": "open", "state": "resolved", "reader": null, "reader_status": "reader_required", "identifier": "10.1016/j.gdata.2015.05.013", "version": null, "note": "Full article fetched from PMC; the checksum covers the rendered section body, not the original XML bytes.", "structure": {"pmcid": "PMC4583631", "source": "europe_pmc_fulltext", "coverage": "whole_body_without_references", "text_hash_scope": "rendered_section_body"}}, {"id": "data:geo:GSE66822", "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=GSE66822", "sha256": null, "bytes": null, "access": "open", "state": "resolved", "reader": null, "reader_status": "reader_required", "identifier": "GSE66822", "version": null, "note": "RNA-Seq raw and analyzed data have been deposited in GEO under accession code GSE66822.", "structure": {"repository": "GEO", "access_route": "GEO accession URL", "access_statement_verbatim": "RNA-Seq raw and analyzed data have been deposited in GEO under accession code GSE66822.", "access_statement_kind": "data_availability_statement", "sample_accessions": ["GSM1632696", "GSM1632697", "GSM1632698", "GSM1632699"], "sample_count": 4, "group_sizes": null, "group_sizes_basis": null, "platform": "18635", "taxon": "Mus musculus", "title": "Prmt5 is a crucial regulator of muscle stem cell expansion in adult mice", "resolution_checked_at": "2026-11-01T15:39:55Z", "resolution_check": "identifier_resolution_only_no_download_no_licence_read", "downloaded": false, "licence_read": false}}, {"id": "asset:table:pmid:26484239:1", "role": "table", "format": "jats-table", "media_type": "application/vnd.jats.table+json", "uri": null, "sha256": "sha256:1803a72ff84202ea1485b12b7efd9d6f5c8f8f44e6d6f5cde2c0cd1d1c547ec9", "bytes": 702, "access": "open", "state": "verified", "reader": "read_table", "reader_status": "available", "identifier": "section[1]/table-wrap[1]#t0010", "version": null, "note": null, "structure": {"pmcid": "PMC4583631", "section_index": 1, "section_title": "p", "row_count": 8, "column_count": 2}, "table": {"label": null, "caption": null, "rows": [["Specifications"], ["Organism/cell line/tissue", "Murine satellite cells (Pax7CreERT2/Prmt5loxP/loxP)"], ["Sequencer or array type", "IonTorrent Proton"], ["Data format", "Raw and analyzed RNA-Seq data"], ["Experimental factors", "Wildtype, Prmt5-knockout"], ["Experimental features", "Arginine methyltransferase Prmt5 was inactivated in isolated MuSCs from adult mice (Pax7CreERT2/Prmt5 loxP/loxP + TAM) and compared to the control condition (Pax7CreERT2/Prmt5+/loxP + TAM) using RNA-Seq."], ["Consent", "Not applicable"], ["Sample source location", "Not applicable"]], "row_count": 8, "column_count": 2, "numeric_cells": 0, "header_rows": 1, "locator": "section[1]/table-wrap[1]#t0010"}}], "gaps": ["asset:data:geo:GSE66822 not downloaded", "asset:data:geo:GSE66822 licence not read"]}, "analysis": {"state": "complete", "methods": [{"id": "method-1", "family": "differential_expression", "specific": "deseq2", "label": "Differential expression analysis", "dsl_operations": ["normalise_counts", "differential_expression_fit", "fdr_bh"], "missing_operations": [], "expressible": true, "parameters": {}, "data_shapes": ["count_matrix_with_condition"], "evidence": {"score": 1.0, "band": "verbatim", "quote": "Differentially expressed genes were identified using DESeq2 version 1.62 [8]."}}], "targets": [], "gaps": []}, "capability": {"state": "complete", "requirements": [{"capability_id": "capability:computational_analysis", "label": "Computational analysis platform", "assay_families": ["meta_analysis", "machine_learning", "survival_analysis", "statistical_regression", "pca", "molecular_docking", "network_analysis", "differential_expression", "gwas"], "availability_state": "owned", "tier_unlocked": "R1", "candidate": "Automated Assays Laravel application and simulated adapters"}], "gaps": []}, "readiness": {"state": "complete", "tier": "R1", "blocking_axis": "none", "blocked_on": "nothing:replicable_now", "axes": {"method": {"tier": "R1", "expressible": true, "required_operations": ["normalise_counts", "differential_expression_fit", "fdr_bh"], "missing_operations": [], "basis": "The paper names the method it used and the corpus's method extractor maps it onto the DSL catalogue: deseq2."}, "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": ["GSE66822"], "resolved_accessions": ["GSE66822"], "statements": ["RNA-Seq raw and analyzed data have been deposited in GEO under accession code GSE66822."], "basis": "The paper names GSE66822 in GEO and the accession resolves in the repository. No dataset was downloaded and no licence was read."}}, "can_run": {"dsl_operations": ["normalise_counts", "differential_expression_fit", "fdr_bh"], "assets": ["source:pmid:26484239", "data:geo:GSE66822", "asset:table:pmid:26484239:1"], "steps": ["run_analysis"]}, "must_build": {"dsl_operations": [], "converters": [], "readers": [], "capabilities": [], "data_gaps": ["data:geo:GSE66822"]}, "gaps": []}, "review": {"state": "partial", "machine_critique": {"kind": "extraction_review", "reader": {"model": "MiniMax-M3.1-Flash", "provider": "minimax", "provider_family": "minimax", "read_at": "2026-10-31T18:25:50Z", "independence": "same_provider"}, "evidence_check": {"method": "verbatim", "availability": "verbatim"}, "calls": 8, "usage": {"prompt_tokens": 17525, "completion_tokens": 2172, "cached_tokens": 1840}}, "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:26484239", "type": "paper", "label": "pmid:26484239"}, {"id": "source:pmid:26484239", "type": "manuscript", "label": "PMID 26484239 full text"}, {"id": "data:geo:GSE66822", "type": "dataset", "label": "GEO GSE66822"}], "activities": [{"id": "activity-reading-sci-2026-11-01", "type": "classification", "used": [{"id": "pmid:26484239", "type": "paper", "label": "pmid:26484239"}, {"id": "source:pmid:26484239", "type": "manuscript", "label": "PMID 26484239 full text"}, {"id": "data:geo:GSE66822", "type": "dataset", "label": "GEO GSE66822"}], "agent": "agent:corpus-assay-engine"}, {"id": "activity-read-26484239", "type": "extraction", "used": ["source:pmid:26484239"], "agent": "agent:minimax-reader"}, {"id": "activity-resolve-GSE66822", "type": "accession_resolution", "used": ["data:geo:GSE66822"], "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:26484239", "parent_hash": "sha256:d1994442e860067406f88082b23056cb4df5008b6b62f197b2076313d62340e6", "fork_of": null, "generation": 7}, "gaps": ["asset:data:geo:GSE66822 licence not read", "asset:data:geo:GSE66822 not downloaded", "execution.not_run", "review.human_critique", "review.independent_reader", "review.machine_critique"], "assays": [{"role": "data_generation", "definition_id": "rna_seq", "definition_version": "99e1195c7d6f", "definition_digest": null, "required_operations": [], "support_state": "partial", "source_hashes": {"assay_lexicon": "99e1195c7d6f"}, "confidence": 0.99, "evidence": ["RNA-Seq analysis of isolated satellite cells in Prmt", "ERT2)/Prmt5(loxP/loxP) knockout mouse model. RNA-Seq raw and analyzed data have been deposited in", "libraries were prepared using the Ion Total RNA-Seq Kit v2 (Life Technologies) with minor change"], "order_basis": "paper_text_order:0", "id": "assay:1"}, {"role": "data_generation", "definition_id": "animal_model", "definition_version": "99e1195c7d6f", "definition_digest": null, "required_operations": [], "support_state": "partial", "source_hashes": {"assay_lexicon": "99e1195c7d6f"}, "confidence": 0.99, "evidence": ["the Pax7(CreERT2)/Prmt5(loxP/loxP) knockout mouse model. RNA-Seq raw and analyzed data have been dep", "the Pax7(CreERT2)/Prmt5(loxP/loxP) knockout mouse model. RNA-Seq raw and analyzed data have be", "xP/loxP mice and two Pax7CreERT2/Prmt5+/loxP mice were used to isolate satellite cells by dissectio"], "order_basis": "paper_text_order:1551", "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": ["y dissection of hind limb muscle followed by FACS sorting using genetic markers or staining of", "erformed as previously described [1]. RNA of FACS sorted satellite cells from mutant (Pax7CreE"], "order_basis": "paper_text_order:1870", "id": "assay:3"}, {"role": "analysis", "definition_id": "differential_expression", "definition_version": "f2132e96ae6c7a4e", "definition_digest": null, "required_operations": ["normalise_counts", "differential_expression_fit", "fdr_bh"], "support_state": "supported", "source_hashes": {"dsl_catalogue": "f2132e96ae6c7a4e"}, "confidence": 1.0, "evidence": ["Differentially expressed genes were identified using DESeq2 version 1.62 [8]."], "order_basis": "consumes_earlier_output", "id": "assay:4"}]}