{
"@context": "/terms/",
"@id": "/measurement-sets/IGVFDS6935HPTC/",
"@type": [
"MeasurementSet",
"FileSet",
"Item"
],
"accession": "IGVFDS6935HPTC",
"aliases": [
"jay-shendure:dev_CRE_mEBs_repA_bulk_RNA_day20_reads"
],
"assay_term": {
"@id": "/assay-terms/OBI_0002675/",
"status": "released",
"term_name": "massively parallel reporter assay"
},
"audit": {
"INTERNAL_ACTION": [
{
"category": "missing sequence specification",
"detail": "Measurement set [IGVFDS6935HPTC](/measurement-sets/IGVFDS6935HPTC/) has sequence file(s): [IGVFFI1858KAHK](/sequence-files/IGVFFI1858KAHK/), [IGVFFI5682PQWU](/sequence-files/IGVFFI5682PQWU/), [IGVFFI0698XKJF](/sequence-files/IGVFFI0698XKJF/) which do not have any `seqspecs`. Sequence files in a file set are expected to link to a sequence specification file.",
"level": 30,
"level_name": "INTERNAL_ACTION",
"name": "audit_missing_seqspec",
"path": "/measurement-sets/IGVFDS6935HPTC/"
},
{
"category": "missing sequence specification",
"detail": "Auxiliary set [IGVFDS0034QRTM](/auxiliary-sets/IGVFDS0034QRTM/) has sequence file(s): [IGVFFI3634UQCG](/sequence-files/IGVFFI3634UQCG/), [IGVFFI1532QXOT](/sequence-files/IGVFFI1532QXOT/), [IGVFFI3468UMEB](/sequence-files/IGVFFI3468UMEB/) which do not have any `seqspecs`. Sequence files in a file set are expected to link to a sequence specification file.",
"level": 30,
"level_name": "INTERNAL_ACTION",
"name": "audit_missing_seqspec",
"path": "/auxiliary-sets/IGVFDS0034QRTM/"
}
]
},
"auxiliary_sets": [
{
"@id": "/auxiliary-sets/IGVFDS0034QRTM/",
"accession": "IGVFDS0034QRTM",
"aliases": [
"jay-shendure:dev_CRE_mEBs_repA_bulk_DNA_day20_reads"
],
"file_set_type": "quantification DNA barcode sequencing",
"status": "released"
}
],
"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": "2023-12-08T23:53:58.704458+00:00",
"donors": [
{
"@id": "/rodent-donors/IGVFDO3898MNLZ/",
"accession": "IGVFDO3898MNLZ",
"aliases": [
"jay-shendure:WD44_donor"
],
"sex": "male",
"status": "released",
"taxa": "Mus musculus"
}
],
"externally_hosted": false,
"file_set_type": "experimental data",
"files": [
{
"@id": "/sequence-files/IGVFFI1858KAHK/",
"accession": "IGVFFI1858KAHK",
"aliases": [
"jay-shendure:bulkMPRA_devCRE_mEBs_repA_day20_RNA_R2"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2023-12-09T00:55:35.474848+00:00",
"file_format": "fastq",
"file_size": 507666276,
"href": "/sequence-files/IGVFFI1858KAHK/@@download/IGVFFI1858KAHK.fastq.gz",
"s3_uri": "s3://igvf-files/2023/12/09/3f2f233a-69f1-477e-bab4-0bd48655c103/IGVFFI1858KAHK.fastq.gz",
"sequencing_platform": {
"@id": "/platform-terms/EFO_0010963/",
"status": "released",
"term_name": "Illumina NextSeq 2000"
},
"status": "released",
"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_d20_RNA_R2_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI5682PQWU/",
"accession": "IGVFFI5682PQWU",
"aliases": [
"jay-shendure:bulkMPRA_devCRE_mEBs_repA_day20_RNA_R1"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2023-12-09T00:55:34.372161+00:00",
"file_format": "fastq",
"file_size": 576923065,
"href": "/sequence-files/IGVFFI5682PQWU/@@download/IGVFFI5682PQWU.fastq.gz",
"s3_uri": "s3://igvf-files/2023/12/09/779fc8db-2a1b-4161-b820-dd3a24385444/IGVFFI5682PQWU.fastq.gz",
"sequencing_platform": {
"@id": "/platform-terms/EFO_0010963/",
"status": "released",
"term_name": "Illumina NextSeq 2000"
},
"status": "released",
"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_d20_RNA_R1_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI0698XKJF/",
"accession": "IGVFFI0698XKJF",
"aliases": [
"jay-shendure:bulkMPRA_devCRE_mEBs_repA_day20_RNA_R3"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2023-12-09T00:55:37.076205+00:00",
"file_format": "fastq",
"file_size": 587546799,
"href": "/sequence-files/IGVFFI0698XKJF/@@download/IGVFFI0698XKJF.fastq.gz",
"s3_uri": "s3://igvf-files/2023/12/09/bef6bbd4-11c3-4e69-80b6-34df12e5e365/IGVFFI0698XKJF.fastq.gz",
"sequencing_platform": {
"@id": "/platform-terms/EFO_0010963/",
"status": "released",
"term_name": "Illumina NextSeq 2000"
},
"status": "released",
"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_d20_RNA_R3_001.fastq.gz",
"upload_status": "validated"
}
],
"input_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"
],
"status": "released"
}
],
"release_timestamp": "2024-06-27T00:41:15.258160+00:00",
"samples": [
{
"@id": "/in-vitro-systems/IGVFSM7918INCH/",
"@type": [
"InVitroSystem",
"Biosample",
"Sample",
"Item"
],
"accession": "IGVFSM7918INCH",
"aliases": [
"jay-shendure:dev_CRE_mEBs_repA_bulk_day20"
],
"cell_fate_change_treatments": [
{
"@id": "/treatments/9acc7857-c9dd-4b4a-a78b-fdf10c8ae679/",
"purpose": "differentiation",
"status": "released",
"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",
"status": "released",
"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 20 days, male, Mus musculus WD44 transfected with a reporter library",
"targeted_sample_term": {
"@id": "/sample-terms/UBERON_0014374/",
"status": "released",
"term_name": "embryoid body"
},
"taxa": "Mus musculus"
}
],
"schema_version": "23",
"status": "released",
"submitted_by": {
"@id": "/users/73f58e9f-8f5d-4fee-a7cd-dd63c0167e4b/",
"title": "Beth Martin"
},
"submitted_files_timestamp": "2023-12-09T00:55:30.593099+00:00",
"summary": "MPRA integrating a reporter library targeting accessible genome regions in many genomic loci",
"uuid": "85b1992c-6892-4bf9-a201-c05eb3fab027"
}