{
"@context": "/terms/",
"@id": "/measurement-sets/IGVFDS3958ZVDP/",
"@type": [
"MeasurementSet",
"FileSet",
"Item"
],
"accession": "IGVFDS3958ZVDP",
"aliases": [
"jay-shendure:dev_CRE_mEBs_repA_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 [IGVFSM8160AXXB](/in-vitro-systems/IGVFSM8160AXXB/) 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/IGVFSM8160AXXB/"
}
],
"NOT_COMPLIANT": [
{
"category": "missing sequence specification",
"detail": "Measurement set [IGVFDS3958ZVDP](/measurement-sets/IGVFDS3958ZVDP/) has sequence file(s): [IGVFFI6209VSOR](/sequence-files/IGVFFI6209VSOR/), [IGVFFI1847EZGR](/sequence-files/IGVFFI1847EZGR/), [IGVFFI1948QSDA](/sequence-files/IGVFFI1948QSDA/) 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/IGVFDS3958ZVDP/"
},
{
"category": "missing sequence specification",
"detail": "Auxiliary set [IGVFDS3729YOSL](/auxiliary-sets/IGVFDS3729YOSL/) has sequence file(s): [IGVFFI3608LRNG](/sequence-files/IGVFFI3608LRNG/), [IGVFFI1604BKDP](/sequence-files/IGVFFI1604BKDP/), [IGVFFI5994ASUH](/sequence-files/IGVFFI5994ASUH/) 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/IGVFDS3729YOSL/"
}
]
},
"auxiliary_sets": [
{
"@id": "/auxiliary-sets/IGVFDS3729YOSL/",
"accession": "IGVFDS3729YOSL",
"aliases": [
"jay-shendure:dev_CRE_mEBs_repA_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": "2023-12-08T23:53:54.167814+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/IGVFFI6209VSOR/",
"accession": "IGVFFI6209VSOR",
"aliases": [
"jay-shendure:bulkMPRA_devCRE_mEBs_repA_day6_RNA_R1"
],
"content_type": "reads",
"creation_timestamp": "2023-12-09T00:54:31.595064+00:00",
"file_format": "fastq",
"file_size": 118911561,
"href": "/sequence-files/IGVFFI6209VSOR/@@download/IGVFFI6209VSOR.fastq.gz",
"s3_uri": "s3://igvf-files/2023/12/09/569a2ce8-85d2-472e-b726-190ac0847ff5/IGVFFI6209VSOR.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_d06_RNA_R1_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI1847EZGR/",
"accession": "IGVFFI1847EZGR",
"aliases": [
"jay-shendure:bulkMPRA_devCRE_mEBs_repA_day6_RNA_R3"
],
"content_type": "reads",
"creation_timestamp": "2023-12-09T00:54:33.924961+00:00",
"file_format": "fastq",
"file_size": 119973915,
"href": "/sequence-files/IGVFFI1847EZGR/@@download/IGVFFI1847EZGR.fastq.gz",
"s3_uri": "s3://igvf-files/2023/12/09/34b5679f-1694-4cf5-a315-a4852cd70f44/IGVFFI1847EZGR.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_d06_RNA_R3_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI1948QSDA/",
"accession": "IGVFFI1948QSDA",
"aliases": [
"jay-shendure:bulkMPRA_devCRE_mEBs_repA_day6_RNA_R2"
],
"content_type": "reads",
"creation_timestamp": "2023-12-09T00:54:32.815365+00:00",
"file_format": "fastq",
"file_size": 98481028,
"href": "/sequence-files/IGVFFI1948QSDA/@@download/IGVFFI1948QSDA.fastq.gz",
"s3_uri": "s3://igvf-files/2023/12/09/9df7878a-3fa3-4399-a693-fcce7e576f2d/IGVFFI1948QSDA.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_d06_RNA_R2_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": "2024-06-27T00:41:14.708829+00:00",
"samples": [
{
"@id": "/in-vitro-systems/IGVFSM8160AXXB/",
"@type": [
"InVitroSystem",
"Biosample",
"Sample",
"Item"
],
"accession": "IGVFSM8160AXXB",
"aliases": [
"jay-shendure:dev_CRE_mEBs_repA_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": "2023-12-09T00:54:27.353774+00:00",
"summary": "MPRA integrating a reporter library targeting accessible genome regions in many genomic loci",
"uuid": "25df76ca-c78b-4010-bfcf-d50146e7fca3"
}