{
"@context": "/terms/",
"@id": "/measurement-sets/IGVFDS9654ACTQ/",
"@type": [
"MeasurementSet",
"FileSet",
"Item"
],
"accession": "IGVFDS9654ACTQ",
"aliases": [
"jay-shendure:dev_CRE_mEBs_repA_bulk_RNA_day16_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 [IGVFSM8231RSVA](/in-vitro-systems/IGVFSM8231RSVA/) 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/IGVFSM8231RSVA/"
}
],
"NOT_COMPLIANT": [
{
"category": "missing sequence specification",
"detail": "Measurement set [IGVFDS9654ACTQ](/measurement-sets/IGVFDS9654ACTQ/) has sequence file(s): [IGVFFI6973TJVY](/sequence-files/IGVFFI6973TJVY/), [IGVFFI8314GMST](/sequence-files/IGVFFI8314GMST/), [IGVFFI5916XKXF](/sequence-files/IGVFFI5916XKXF/), [IGVFFI4135CDDC](/sequence-files/IGVFFI4135CDDC/), [IGVFFI2792RJXL](/sequence-files/IGVFFI2792RJXL/), [IGVFFI1530ZOZF](/sequence-files/IGVFFI1530ZOZF/) 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/IGVFDS9654ACTQ/"
},
{
"category": "missing sequence specification",
"detail": "Auxiliary set [IGVFDS8347TPDV](/auxiliary-sets/IGVFDS8347TPDV/) has sequence file(s): [IGVFFI3245JMHQ](/sequence-files/IGVFFI3245JMHQ/), [IGVFFI7612SSEB](/sequence-files/IGVFFI7612SSEB/), [IGVFFI8153ZVNU](/sequence-files/IGVFFI8153ZVNU/), [IGVFFI6464LXPC](/sequence-files/IGVFFI6464LXPC/), [IGVFFI9484FOLM](/sequence-files/IGVFFI9484FOLM/), [IGVFFI0800YEAV](/sequence-files/IGVFFI0800YEAV/) 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/IGVFDS8347TPDV/"
}
]
},
"auxiliary_sets": [
{
"@id": "/auxiliary-sets/IGVFDS8347TPDV/",
"accession": "IGVFDS8347TPDV",
"aliases": [
"jay-shendure:dev_CRE_mEBs_repA_bulk_DNA_day16_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": "2023-12-08T23:53:57.412061+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/IGVFFI6973TJVY/",
"accession": "IGVFFI6973TJVY",
"aliases": [
"jay-shendure:bulkMPRA_devCRE_mEBs_repA_day16_RNA_R2"
],
"content_type": "reads",
"creation_timestamp": "2023-12-09T00:55:20.188745+00:00",
"file_format": "fastq",
"file_size": 136570630,
"href": "/sequence-files/IGVFFI6973TJVY/@@download/IGVFFI6973TJVY.fastq.gz",
"s3_uri": "s3://igvf-files/2023/12/09/9e25748b-1f63-49ad-b485-0b11e909fde5/IGVFFI6973TJVY.fastq.gz",
"sequencing_platform": {
"@id": "/platform-terms/EFO_0009173/",
"term_name": "Illumina NextSeq 500"
},
"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_d16_RNA_R2_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI8314GMST/",
"accession": "IGVFFI8314GMST",
"aliases": [
"jay-shendure:bulkMPRA_devCRE_mEBs_repA_day16_RNA_R1"
],
"content_type": "reads",
"creation_timestamp": "2023-12-09T00:55:18.821507+00:00",
"file_format": "fastq",
"file_size": 275796088,
"href": "/sequence-files/IGVFFI8314GMST/@@download/IGVFFI8314GMST.fastq.gz",
"s3_uri": "s3://igvf-files/2023/12/09/013bdf70-754b-4e8b-bbaa-4aa159042f43/IGVFFI8314GMST.fastq.gz",
"sequencing_platform": {
"@id": "/platform-terms/EFO_0009173/",
"term_name": "Illumina NextSeq 500"
},
"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_d16_RNA_R1_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI5916XKXF/",
"accession": "IGVFFI5916XKXF",
"aliases": [
"jay-shendure:bulkMPRA_devCRE_mEBs_repA_day16_RNA_R3"
],
"content_type": "reads",
"creation_timestamp": "2023-12-09T00:55:21.414841+00:00",
"file_format": "fastq",
"file_size": 396038632,
"href": "/sequence-files/IGVFFI5916XKXF/@@download/IGVFFI5916XKXF.fastq.gz",
"s3_uri": "s3://igvf-files/2023/12/09/6ca472a4-c2f9-42b7-83a8-ca3f42a757db/IGVFFI5916XKXF.fastq.gz",
"sequencing_platform": {
"@id": "/platform-terms/EFO_0009173/",
"term_name": "Illumina NextSeq 500"
},
"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_d16_RNA_R3_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI4135CDDC/",
"accession": "IGVFFI4135CDDC",
"aliases": [
"jay-shendure:bulkMPRA_devCRE_mEBs_repA_day16_RNA_addreads_R1"
],
"content_type": "reads",
"creation_timestamp": "2023-12-09T00:55:15.244321+00:00",
"file_format": "fastq",
"file_size": 391735598,
"href": "/sequence-files/IGVFFI4135CDDC/@@download/IGVFFI4135CDDC.fastq.gz",
"s3_uri": "s3://igvf-files/2023/12/09/f81ca173-3f56-4712-b8dc-47eb7fcdd3bf/IGVFFI4135CDDC.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_d16_RNA_lib_rep_R1_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI2792RJXL/",
"accession": "IGVFFI2792RJXL",
"aliases": [
"jay-shendure:bulkMPRA_devCRE_mEBs_repA_day16_RNA_addreads_R2"
],
"content_type": "reads",
"creation_timestamp": "2023-12-09T00:55:16.436653+00:00",
"file_format": "fastq",
"file_size": 330509830,
"href": "/sequence-files/IGVFFI2792RJXL/@@download/IGVFFI2792RJXL.fastq.gz",
"s3_uri": "s3://igvf-files/2023/12/09/5476aaef-9106-49b3-bb04-6c868427330f/IGVFFI2792RJXL.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_d16_RNA_lib_rep_R2_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI1530ZOZF/",
"accession": "IGVFFI1530ZOZF",
"aliases": [
"jay-shendure:bulkMPRA_devCRE_mEBs_repA_day16_RNA_addreads_R3"
],
"content_type": "reads",
"creation_timestamp": "2023-12-09T00:55:17.672354+00:00",
"file_format": "fastq",
"file_size": 397512183,
"href": "/sequence-files/IGVFFI1530ZOZF/@@download/IGVFFI1530ZOZF.fastq.gz",
"s3_uri": "s3://igvf-files/2023/12/09/37950888-1f55-48ee-abc9-e5d5e7921ae7/IGVFFI1530ZOZF.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_d16_RNA_lib_rep_R3_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": "2024-06-27T00:41:14.387717+00:00",
"samples": [
{
"@id": "/in-vitro-systems/IGVFSM8231RSVA/",
"@type": [
"InVitroSystem",
"Biosample",
"Sample",
"Item"
],
"accession": "IGVFSM8231RSVA",
"aliases": [
"jay-shendure:dev_CRE_mEBs_repA_bulk_day16"
],
"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 16 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": "2023-12-09T00:55:07.897458+00:00",
"summary": "MPRA integrating a reporter library targeting accessible genome regions in many genomic loci",
"uuid": "d545c14f-52a8-4d42-8d4c-cc7483eca046"
}