{
"@context": "/terms/",
"@id": "/measurement-sets/IGVFDS0115ZUKE/",
"@type": [
"MeasurementSet",
"FileSet",
"Item"
],
"accession": "IGVFDS0115ZUKE",
"aliases": [
"jay-shendure:dev_CRE_mEBs_repB_bulk_RNA_day6_reads"
],
"assay_term": {
"@id": "/assay-terms/OBI_0002675/",
"term_name": "massively parallel reporter assay"
},
"audit": {
"INTERNAL_ACTION": [
{
"category": "mismatched status",
"detail": "Released in vitro system [IGVFSM0374VHIT](/in-vitro-systems/IGVFSM0374VHIT/) has in progress subobject construct library set [IGVFDS7655GRFI](/construct-library-sets/IGVFDS7655GRFI/).",
"level": 30,
"level_name": "INTERNAL_ACTION",
"name": "audit_item_status",
"path": "/in-vitro-systems/IGVFSM0374VHIT/"
}
],
"NOT_COMPLIANT": [
{
"category": "missing sequence specification",
"detail": "Measurement set [IGVFDS0115ZUKE](/measurement-sets/IGVFDS0115ZUKE/) has sequence file(s): [IGVFFI6028ZBUL](/sequence-files/IGVFFI6028ZBUL/), [IGVFFI2528UYLX](/sequence-files/IGVFFI2528UYLX/), [IGVFFI9407AJGY](/sequence-files/IGVFFI9407AJGY/) which do not have any `seqspecs`. Sequence files in a file set are expected to link to a sequence specification file.",
"level": 50,
"level_name": "NOT_COMPLIANT",
"name": "audit_missing_seqspec",
"path": "/measurement-sets/IGVFDS0115ZUKE/"
},
{
"category": "missing sequence specification",
"detail": "Auxiliary set [IGVFDS8519NOEI](/auxiliary-sets/IGVFDS8519NOEI/) has sequence file(s): [IGVFFI5110VCEQ](/sequence-files/IGVFFI5110VCEQ/), [IGVFFI9772ARFL](/sequence-files/IGVFFI9772ARFL/), [IGVFFI2882VBPJ](/sequence-files/IGVFFI2882VBPJ/) which do not have any `seqspecs`. Sequence files in a file set are expected to link to a sequence specification file.",
"level": 50,
"level_name": "NOT_COMPLIANT",
"name": "audit_missing_seqspec",
"path": "/auxiliary-sets/IGVFDS8519NOEI/"
}
]
},
"auxiliary_sets": [
{
"@id": "/auxiliary-sets/IGVFDS8519NOEI/",
"accession": "IGVFDS8519NOEI",
"aliases": [
"jay-shendure:dev_CRE_mEBs_repB_bulk_DNA_day6_reads"
],
"file_set_type": "quantification DNA barcode sequencing"
}
],
"award": {
"@id": "/awards/HG011966/",
"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": "2023-12-08T23:54:02.662249+00:00",
"donors": [
{
"@id": "/rodent-donors/IGVFDO3898MNLZ/",
"accession": "IGVFDO3898MNLZ",
"aliases": [
"jay-shendure:WD44_donor"
],
"sex": "male",
"status": "released",
"taxa": "Mus musculus"
}
],
"file_set_type": "experimental data",
"files": [
{
"@id": "/sequence-files/IGVFFI6028ZBUL/",
"accession": "IGVFFI6028ZBUL",
"aliases": [
"jay-shendure:bulkMPRA_devCRE_mEBs_repB_day6_RNA_R3"
],
"content_type": "reads",
"creation_timestamp": "2023-12-09T00:56:15.044052+00:00",
"file_format": "fastq",
"file_size": 301773032,
"href": "/sequence-files/IGVFFI6028ZBUL/@@download/IGVFFI6028ZBUL.fastq.gz",
"s3_uri": "s3://igvf-files/2023/12/09/d0676b12-01ce-4285-95d5-e2ac58fa240f/IGVFFI6028ZBUL.fastq.gz",
"sequencing_platform": {
"@id": "/platform-terms/EFO_0010963/",
"term_name": "Illumina NextSeq 2000"
},
"submitted_file_name": "/net/shendure/vol8/projects/JBL/GEO_sc_rep_fastqs_nobackup/geo_submission_20221108/bulkMPRA_devCRE_mEBs/bulk_MPRA_mEB_series_mBC_repB_d06_RNA_R3_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI2528UYLX/",
"accession": "IGVFFI2528UYLX",
"aliases": [
"jay-shendure:bulkMPRA_devCRE_mEBs_repB_day6_RNA_R2"
],
"content_type": "reads",
"creation_timestamp": "2023-12-09T00:56:13.757657+00:00",
"file_format": "fastq",
"file_size": 247078032,
"href": "/sequence-files/IGVFFI2528UYLX/@@download/IGVFFI2528UYLX.fastq.gz",
"s3_uri": "s3://igvf-files/2023/12/09/3d95e0b0-cb7e-44f5-a8e3-956f9586fad2/IGVFFI2528UYLX.fastq.gz",
"sequencing_platform": {
"@id": "/platform-terms/EFO_0010963/",
"term_name": "Illumina NextSeq 2000"
},
"submitted_file_name": "/net/shendure/vol8/projects/JBL/GEO_sc_rep_fastqs_nobackup/geo_submission_20221108/bulkMPRA_devCRE_mEBs/bulk_MPRA_mEB_series_mBC_repB_d06_RNA_R2_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI9407AJGY/",
"accession": "IGVFFI9407AJGY",
"aliases": [
"jay-shendure:bulkMPRA_devCRE_mEBs_repB_day6_RNA_R1"
],
"content_type": "reads",
"creation_timestamp": "2023-12-09T00:56:12.117321+00:00",
"file_format": "fastq",
"file_size": 298376998,
"href": "/sequence-files/IGVFFI9407AJGY/@@download/IGVFFI9407AJGY.fastq.gz",
"s3_uri": "s3://igvf-files/2023/12/09/5744207b-9801-48d9-a7fb-cc9b824f6b99/IGVFFI9407AJGY.fastq.gz",
"sequencing_platform": {
"@id": "/platform-terms/EFO_0010963/",
"term_name": "Illumina NextSeq 2000"
},
"submitted_file_name": "/net/shendure/vol8/projects/JBL/GEO_sc_rep_fastqs_nobackup/geo_submission_20221108/bulkMPRA_devCRE_mEBs/bulk_MPRA_mEB_series_mBC_repB_d06_RNA_R1_001.fastq.gz",
"upload_status": "validated"
}
],
"input_file_set_for": [
"/analysis-sets/IGVFDS2622CKLA/"
],
"lab": {
"@id": "/labs/jay-shendure/",
"title": "Jay Shendure, UW"
},
"notes": "The readout b59a5259-3a53-482b-a7a5-6f401bdad220 was removed from this measurement set.",
"preferred_assay_title": "MPRA",
"protocols": [
"https://www.protocols.io/file/n92rb7r27.pdf"
],
"publications": [
{
"@id": "/publications/398edd7f-1ebb-40a0-a04b-450a2565667c/",
"publication_identifiers": [
"doi:10.1038/s41592-024-02260-3",
"PMID:38724692"
]
}
],
"release_timestamp": "2024-06-27T00:41:15.346199+00:00",
"samples": [
{
"@id": "/in-vitro-systems/IGVFSM0374VHIT/",
"@type": [
"InVitroSystem",
"Biosample",
"Sample",
"Item"
],
"accession": "IGVFSM0374VHIT",
"aliases": [
"jay-shendure:dev_CRE_mEBs_repB_bulk_day6"
],
"cell_fate_change_treatments": [
{
"@id": "/treatments/9acc7857-c9dd-4b4a-a78b-fdf10c8ae679/",
"purpose": "differentiation",
"summary": "Depletion of Leukemia inhibitory factor",
"treatment_type": "protein"
}
],
"classifications": [
"differentiated cell specimen"
],
"construct_library_sets": [
{
"@id": "/construct-library-sets/IGVFDS7655GRFI/",
"accession": "IGVFDS7655GRFI",
"file_set_type": "reporter library",
"summary": "Reporter library targeting accessible genome regions in many genomic loci"
}
],
"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 6 days, male, Mus musculus WD44 modified with a reporter library",
"targeted_sample_term": {
"@id": "/sample-terms/UBERON_0014374/",
"term_name": "embryoid body"
},
"taxa": "Mus musculus"
}
],
"schema_version": "21",
"status": "released",
"submitted_by": {
"@id": "/users/73f58e9f-8f5d-4fee-a7cd-dd63c0167e4b/",
"title": "Beth Martin"
},
"submitted_files_timestamp": "2023-12-09T00:56:08.601942+00:00",
"summary": "MPRA integrating a reporter library targeting accessible genome regions in many genomic loci",
"uuid": "9149b734-de72-4926-82f1-67683afd4aa0"
}