{
"@context": "/terms/",
"@id": "/measurement-sets/IGVFDS2290VBBK/",
"@type": [
"MeasurementSet",
"FileSet",
"Item"
],
"accession": "IGVFDS2290VBBK",
"aliases": [
"jay-shendure:dev_CRE_mEBs_repB_bulk_RNA_day2_reads"
],
"assay_term": {
"@id": "/assay-terms/OBI_0002675/",
"status": "released",
"term_name": "massively parallel reporter assay"
},
"audit": {
"INTERNAL_ACTION": [
{
"category": "missing sequence specification",
"detail": "Auxiliary set [IGVFDS2885IUWV](/auxiliary-sets/IGVFDS2885IUWV/) has sequence file(s): [IGVFFI8096RPRG](/sequence-files/IGVFFI8096RPRG/), [IGVFFI1506GBPW](/sequence-files/IGVFFI1506GBPW/), [IGVFFI6813SNVQ](/sequence-files/IGVFFI6813SNVQ/) 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/IGVFDS2885IUWV/"
},
{
"category": "missing sequence specification",
"detail": "Measurement set [IGVFDS2290VBBK](/measurement-sets/IGVFDS2290VBBK/) has sequence file(s): [IGVFFI9082OFME](/sequence-files/IGVFFI9082OFME/), [IGVFFI3367ATPC](/sequence-files/IGVFFI3367ATPC/), [IGVFFI4930EVFR](/sequence-files/IGVFFI4930EVFR/) 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/IGVFDS2290VBBK/"
}
]
},
"auxiliary_sets": [
{
"@id": "/auxiliary-sets/IGVFDS2885IUWV/",
"accession": "IGVFDS2885IUWV",
"aliases": [
"jay-shendure:dev_CRE_mEBs_repB_bulk_DNA_day2_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": "2023-12-08T23:54:01.125912+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/IGVFFI9082OFME/",
"accession": "IGVFFI9082OFME",
"aliases": [
"jay-shendure:bulkMPRA_devCRE_mEBs_repB_day2_RNA_R1"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2023-12-09T00:55:57.509019+00:00",
"file_format": "fastq",
"file_size": 325147969,
"href": "/sequence-files/IGVFFI9082OFME/@@download/IGVFFI9082OFME.fastq.gz",
"s3_uri": "s3://igvf-files/2023/12/09/681e49a5-4d1c-46f9-8be4-62b19057a0d1/IGVFFI9082OFME.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_repB_d02_RNA_R1_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI3367ATPC/",
"accession": "IGVFFI3367ATPC",
"aliases": [
"jay-shendure:bulkMPRA_devCRE_mEBs_repB_day2_RNA_R2"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2023-12-09T00:55:58.739971+00:00",
"file_format": "fastq",
"file_size": 267762025,
"href": "/sequence-files/IGVFFI3367ATPC/@@download/IGVFFI3367ATPC.fastq.gz",
"s3_uri": "s3://igvf-files/2023/12/09/cdedf571-375c-45b2-a8d7-604e88c13d90/IGVFFI3367ATPC.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_repB_d02_RNA_R2_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI4930EVFR/",
"accession": "IGVFFI4930EVFR",
"aliases": [
"jay-shendure:bulkMPRA_devCRE_mEBs_repB_day2_RNA_R3"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2023-12-09T00:55:59.886040+00:00",
"file_format": "fastq",
"file_size": 328635589,
"href": "/sequence-files/IGVFFI4930EVFR/@@download/IGVFFI4930EVFR.fastq.gz",
"s3_uri": "s3://igvf-files/2023/12/09/fbf62e77-eca5-49be-848c-2398c9fbf98b/IGVFFI4930EVFR.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_repB_d02_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": "2024-06-27T00:41:19.227877+00:00",
"samples": [
{
"@id": "/in-vitro-systems/IGVFSM8486OPKV/",
"@type": [
"InVitroSystem",
"Biosample",
"Sample",
"Item"
],
"accession": "IGVFSM8486OPKV",
"aliases": [
"jay-shendure:dev_CRE_mEBs_repB_bulk_day2"
],
"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 2 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": "2023-12-09T00:55:53.759563+00:00",
"summary": "MPRA integrating a reporter library targeting accessible genome regions in many genomic loci",
"uuid": "8ccfc7a8-a9cf-4e71-8cc9-95dad39904b4"
}