{
"@context": "/terms/",
"@id": "/measurement-sets/IGVFDS1567LQJL/",
"@type": [
"MeasurementSet",
"FileSet",
"Item"
],
"accession": "IGVFDS1567LQJL",
"aliases": [
"jay-shendure:dev_CRE_mEBs_repA_bulk_RNA_day2_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 [IGVFSM5738IXAN](/in-vitro-systems/IGVFSM5738IXAN/) 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/IGVFSM5738IXAN/"
}
],
"NOT_COMPLIANT": [
{
"category": "missing sequence specification",
"detail": "Auxiliary set [IGVFDS2513FWFN](/auxiliary-sets/IGVFDS2513FWFN/) has sequence file(s): [IGVFFI2125IYPC](/sequence-files/IGVFFI2125IYPC/), [IGVFFI8950KTPH](/sequence-files/IGVFFI8950KTPH/), [IGVFFI0017WPTX](/sequence-files/IGVFFI0017WPTX/) 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/IGVFDS2513FWFN/"
},
{
"category": "missing sequence specification",
"detail": "Measurement set [IGVFDS1567LQJL](/measurement-sets/IGVFDS1567LQJL/) has sequence file(s): [IGVFFI2329JMRB](/sequence-files/IGVFFI2329JMRB/), [IGVFFI2769TXAA](/sequence-files/IGVFFI2769TXAA/), [IGVFFI1980QMMF](/sequence-files/IGVFFI1980QMMF/) 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/IGVFDS1567LQJL/"
}
]
},
"auxiliary_sets": [
{
"@id": "/auxiliary-sets/IGVFDS2513FWFN/",
"accession": "IGVFDS2513FWFN",
"aliases": [
"jay-shendure:dev_CRE_mEBs_repA_bulk_DNA_day2_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": "2023-12-08T23:53:51.719023+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/IGVFFI2329JMRB/",
"accession": "IGVFFI2329JMRB",
"aliases": [
"jay-shendure:bulkMPRA_devCRE_mEBs_repA_day2_RNA_R2"
],
"content_type": "reads",
"creation_timestamp": "2023-12-09T00:54:17.216628+00:00",
"file_format": "fastq",
"file_size": 175635303,
"href": "/sequence-files/IGVFFI2329JMRB/@@download/IGVFFI2329JMRB.fastq.gz",
"s3_uri": "s3://igvf-files/2023/12/09/dc6e11ad-47c4-47c7-ab4a-0e8529068694/IGVFFI2329JMRB.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_repA_d02_RNA_R2_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI2769TXAA/",
"accession": "IGVFFI2769TXAA",
"aliases": [
"jay-shendure:bulkMPRA_devCRE_mEBs_repA_day2_RNA_R3"
],
"content_type": "reads",
"creation_timestamp": "2023-12-09T00:54:18.339508+00:00",
"file_format": "fastq",
"file_size": 219991545,
"href": "/sequence-files/IGVFFI2769TXAA/@@download/IGVFFI2769TXAA.fastq.gz",
"s3_uri": "s3://igvf-files/2023/12/09/fc740a95-580b-4edf-a96d-1198583b15c4/IGVFFI2769TXAA.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_repA_d02_RNA_R3_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI1980QMMF/",
"accession": "IGVFFI1980QMMF",
"aliases": [
"jay-shendure:bulkMPRA_devCRE_mEBs_repA_day2_RNA_R1"
],
"content_type": "reads",
"creation_timestamp": "2023-12-09T00:54:15.933307+00:00",
"file_format": "fastq",
"file_size": 214677348,
"href": "/sequence-files/IGVFFI1980QMMF/@@download/IGVFFI1980QMMF.fastq.gz",
"s3_uri": "s3://igvf-files/2023/12/09/8ec622c5-c258-4a11-93d3-92a96a7129b8/IGVFFI1980QMMF.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_repA_d02_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": "2024-06-27T00:41:14.526583+00:00",
"samples": [
{
"@id": "/in-vitro-systems/IGVFSM5738IXAN/",
"@type": [
"InVitroSystem",
"Biosample",
"Sample",
"Item"
],
"accession": "IGVFSM5738IXAN",
"aliases": [
"jay-shendure:dev_CRE_mEBs_repA_bulk_day2"
],
"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 2 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": "2023-12-09T00:54:12.154681+00:00",
"summary": "MPRA integrating a reporter library targeting accessible genome regions in many genomic loci",
"uuid": "2ecce5a6-e357-4188-886f-7e09da1b1ebd"
}