{
"@context": "/terms/",
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"FileSet",
"Item"
],
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"jay-shendure:analysis_set_scATAC_mEBs"
],
"assay_titles": [
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],
"audit": {
"WARNING": [
{
"category": "missing analysis step version",
"detail": "Analysis set [IGVFDS7801YPEU](/analysis-sets/IGVFDS7801YPEU/) links to file(s) [IGVFFI9468KRLQ](/signal-files/IGVFFI9468KRLQ/), [IGVFFI4530JOCA](/signal-files/IGVFFI4530JOCA/), [IGVFFI4106YTGZ](/signal-files/IGVFFI4106YTGZ/), [IGVFFI6250RJNE](/signal-files/IGVFFI6250RJNE/), [IGVFFI4871DVXE](/signal-files/IGVFFI4871DVXE/), [IGVFFI8400FXRX](/signal-files/IGVFFI8400FXRX/), [IGVFFI9916JAHE](/signal-files/IGVFFI9916JAHE/) that are missing `analysis_step_version`. Analysis set files are expected to specify analysis step version.",
"level": 40,
"level_name": "WARNING",
"name": "audit_analysis_set_files_missing_analysis_step_version",
"path": "/analysis-sets/IGVFDS7801YPEU/"
}
]
},
"award": {
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"component": "functional characterization",
"contact_pi": {
"@id": "/users/eb543cda-67b7-493c-84eb-187d0dac13ba/",
"title": "Jay Shendure"
},
"title": "Massively parallel characterization of variants and elements impacting transcriptional regulation in dynamic cellular systems"
},
"control_for": [],
"creation_timestamp": "2023-12-12T23:07:36.353419+00:00",
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{
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"aliases": [
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],
"sex": "male",
"status": "released",
"taxa": "Mus musculus"
}
],
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},
{
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},
{
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"aliases": [
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],
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"upload_status": "validated"
},
{
"@id": "/signal-files/IGVFFI6250RJNE/",
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"aliases": [
"jay-shendure:scATAC_mEBs_bigwig_mesoderm"
],
"assembly": "GRCm39",
"content_type": "signal",
"creation_timestamp": "2024-07-01T19:59:15.664731+00:00",
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},
{
"@id": "/signal-files/IGVFFI4871DVXE/",
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"upload_status": "validated"
},
{
"@id": "/signal-files/IGVFFI8400FXRX/",
"accession": "IGVFFI8400FXRX",
"aliases": [
"jay-shendure:scATAC_mEBs_bigwig_pluripotent_epiblast"
],
"assembly": "GRCm39",
"content_type": "signal",
"creation_timestamp": "2024-07-01T19:59:19.158149+00:00",
"file_format": "bigWig",
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"submitted_file_name": "/net/shendure/vol8/projects/JBL/GEO_scATAC_EB_correction_nobackup/bigwigs/pluripotent_epiblast-TileSize-50-normMethod-ReadsInTSS-ArchR_mm39.bw",
"upload_status": "validated"
},
{
"@id": "/signal-files/IGVFFI9916JAHE/",
"accession": "IGVFFI9916JAHE",
"aliases": [
"jay-shendure:scATAC_mEBs_bigwig_surface_ectoderm"
],
"assembly": "GRCm39",
"content_type": "signal",
"creation_timestamp": "2024-07-01T19:59:21.029721+00:00",
"file_format": "bigWig",
"file_size": 76506261,
"href": "/signal-files/IGVFFI9916JAHE/@@download/IGVFFI9916JAHE.bigWig",
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"submitted_file_name": "/net/shendure/vol8/projects/JBL/GEO_scATAC_EB_correction_nobackup/bigwigs/surface_ectoderm-TileSize-50-normMethod-ReadsInTSS-ArchR_mm39.bw",
"upload_status": "validated"
}
],
"functional_assay_mechanisms": [],
"input_file_sets": [
{
"@id": "/measurement-sets/IGVFDS1560LMQZ/",
"accession": "IGVFDS1560LMQZ",
"aliases": [
"jay-shendure:scATAC_mEBs_rep1_10XlaneA_reads"
],
"file_set_type": "experimental data"
},
{
"@id": "/measurement-sets/IGVFDS6675BDQA/",
"accession": "IGVFDS6675BDQA",
"aliases": [
"jay-shendure:scATAC_mEBs_rep1_10XlaneB_reads"
],
"file_set_type": "experimental data"
},
{
"@id": "/measurement-sets/IGVFDS7446XPVQ/",
"accession": "IGVFDS7446XPVQ",
"aliases": [
"jay-shendure:scATAC_mEBs_rep2_10XlaneA_reads"
],
"file_set_type": "experimental data"
},
{
"@id": "/measurement-sets/IGVFDS0935XBYS/",
"accession": "IGVFDS0935XBYS",
"aliases": [
"jay-shendure:scATAC_mEBs_rep2_10XlaneB_reads"
],
"file_set_type": "experimental data"
}
],
"input_for": [],
"lab": {
"@id": "/labs/jay-shendure/",
"title": "Jay Shendure, UW"
},
"notes": "This object's file_set_type was primary analysis and has been updated to be principal analysis.",
"protocols": [
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],
"publications": [
{
"@id": "/publications/398edd7f-1ebb-40a0-a04b-450a2565667c/",
"publication_identifiers": [
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"PMID:38724692"
]
}
],
"release_timestamp": "2024-07-09T20:16:41.420386+00:00",
"sample_summary": "mouse embryonic stem cell differentiated cell specimen induced to embryoid body, at 1 time point(s) post change",
"samples": [
{
"@id": "/in-vitro-systems/IGVFSM4284RDJK/",
"@type": [
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"Biosample",
"Sample",
"Item"
],
"accession": "IGVFSM4284RDJK",
"aliases": [
"jay-shendure:scATAC_mEBs_rep2_10XlaneB"
],
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],
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],
"sample_terms": [
{
"@id": "/sample-terms/EFO_0004038/",
"@type": [
"SampleTerm",
"OntologyTerm",
"Item"
],
"status": "released",
"summary": "mouse embryonic stem cell",
"term_name": "mouse embryonic stem cell"
}
],
"status": "released",
"summary": "mouse embryonic stem differentiated cell specimen induced to embryoid body for 21 days (cellular sub pool: 10XlaneB), male, Mus musculus WD44",
"targeted_sample_term": {
"@id": "/sample-terms/UBERON_0014374/",
"term_name": "embryoid body"
},
"taxa": "Mus musculus"
},
{
"@id": "/in-vitro-systems/IGVFSM9475FJUV/",
"@type": [
"InVitroSystem",
"Biosample",
"Sample",
"Item"
],
"accession": "IGVFSM9475FJUV",
"aliases": [
"jay-shendure:scATAC_mEBs_rep1_10XlaneA"
],
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"Item"
],
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"summary": "mouse embryonic stem cell",
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}
],
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"summary": "mouse embryonic stem differentiated cell specimen induced to embryoid body for 21 days (cellular sub pool: 10XlaneA), male, Mus musculus WD44",
"targeted_sample_term": {
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"term_name": "embryoid body"
},
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},
{
"@id": "/in-vitro-systems/IGVFSM7126ZMPT/",
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"Biosample",
"Sample",
"Item"
],
"accession": "IGVFSM7126ZMPT",
"aliases": [
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],
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{
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"OntologyTerm",
"Item"
],
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}
],
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"targeted_sample_term": {
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"term_name": "embryoid body"
},
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},
{
"@id": "/in-vitro-systems/IGVFSM6820XJKR/",
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"Biosample",
"Sample",
"Item"
],
"accession": "IGVFSM6820XJKR",
"aliases": [
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],
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"OntologyTerm",
"Item"
],
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}
],
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"targeted_sample_term": {
"@id": "/sample-terms/UBERON_0014374/",
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},
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}
],
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"title": "Beth Martin"
},
"submitted_files_timestamp": "2024-07-01T19:59:09.801166+00:00",
"summary": "scATAC-seq: signal",
"uuid": "c69d7cb4-f432-4b38-b99c-7233b7d96af5",
"workflows": []
}