{
"@context": "/terms/",
"@id": "/auxiliary-sets/IGVFDS7168JGPF/",
"@type": [
"AuxiliarySet",
"FileSet",
"Item"
],
"accession": "IGVFDS7168JGPF",
"aliases": [
"jay-shendure:dev_CRE_mEBs_mBC_repB_10Xlane1_reads"
],
"audit": {},
"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": "2023-12-08T23:52:10.808110+00:00",
"donors": [
{
"@id": "/rodent-donors/IGVFDO3898MNLZ/",
"accession": "IGVFDO3898MNLZ",
"aliases": [
"jay-shendure:WD44_donor"
],
"sex": "male",
"status": "released",
"taxa": "Mus musculus"
}
],
"file_set_type": "quantification DNA barcode sequencing",
"files": [
{
"@id": "/sequence-files/IGVFFI6784ZGTO/",
"accession": "IGVFFI6784ZGTO",
"aliases": [
"jay-shendure:sc_rep_devCRE_mEBs_mBC_pdT_repB_10Xlane1_R1"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2023-12-09T00:58:36.539181+00:00",
"file_format": "fastq",
"file_size": 929041733,
"href": "/sequence-files/IGVFFI6784ZGTO/@@download/IGVFFI6784ZGTO.fastq.gz",
"s3_uri": "s3://igvf-files/2023/12/09/d83d56cd-a616-4fd0-8ec3-0bfdda53e77b/IGVFFI6784ZGTO.fastq.gz",
"sequencing_platform": "/platform-terms/EFO_0009173/",
"status": "released",
"submitted_file_name": "/net/shendure/vol8/projects/JBL/GEO_sc_rep_fastqs_nobackup/geo_submission_20221108/sc_rep_devCRE_mEBs/sc_rep_mEB_series_mBC_pdT_repB_lane1_R1_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI4393QBVG/",
"accession": "IGVFFI4393QBVG",
"aliases": [
"jay-shendure:sc_rep_devCRE_mEBs_mBC_pdT_repB_10Xlane1_R2"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2023-12-09T00:58:37.767264+00:00",
"file_format": "fastq",
"file_size": 1021730671,
"href": "/sequence-files/IGVFFI4393QBVG/@@download/IGVFFI4393QBVG.fastq.gz",
"s3_uri": "s3://igvf-files/2023/12/09/5f57b4a6-2093-4a3d-9743-cdcf292e2ba9/IGVFFI4393QBVG.fastq.gz",
"sequencing_platform": "/platform-terms/EFO_0009173/",
"status": "released",
"submitted_file_name": "/net/shendure/vol8/projects/JBL/GEO_sc_rep_fastqs_nobackup/geo_submission_20221108/sc_rep_devCRE_mEBs/sc_rep_mEB_series_mBC_pdT_repB_lane1_R2_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI0877RZRS/",
"accession": "IGVFFI0877RZRS",
"aliases": [
"jay-shendure:sc_rep_devCRE_mEBs_mBC_pdT_repB_10Xlane1_I1"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2023-12-09T00:58:35.317091+00:00",
"file_format": "fastq",
"file_size": 313749879,
"href": "/sequence-files/IGVFFI0877RZRS/@@download/IGVFFI0877RZRS.fastq.gz",
"s3_uri": "s3://igvf-files/2023/12/09/c6af5d97-cfd5-460e-888f-b0a89f9bf641/IGVFFI0877RZRS.fastq.gz",
"sequencing_platform": "/platform-terms/EFO_0009173/",
"status": "released",
"submitted_file_name": "/net/shendure/vol8/projects/JBL/GEO_sc_rep_fastqs_nobackup/geo_submission_20221108/sc_rep_devCRE_mEBs/sc_rep_mEB_series_mBC_pdT_repB_lane1_I1_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/configuration-files/IGVFFI0199EHIM/",
"accession": "IGVFFI0199EHIM",
"aliases": [
"jay-shendure:seqspec_of_set_IGVFDS7168JGPF"
],
"content_type": "seqspec",
"creation_timestamp": "2024-08-22T22:51:19.537688+00:00",
"file_format": "yaml",
"file_size": 1105,
"href": "/configuration-files/IGVFFI0199EHIM/@@download/IGVFFI0199EHIM.yaml.gz",
"s3_uri": "s3://igvf-files/2024/08/22/1663b0be-218e-46c6-9d8a-bebd67db97ce/IGVFFI0199EHIM.yaml.gz",
"status": "in progress",
"submitted_file_name": "/net/shendure/vol1/home/martin91/IGVF/forupload/seqspecs/scQers/scQers_IGVFDS7168JGPF_seqspec.yaml.gz",
"upload_status": "validated"
}
],
"input_for": [
"/analysis-sets/IGVFDS2774OLAH/"
],
"lab": {
"@id": "/labs/jay-shendure/",
"title": "Jay Shendure, UW"
},
"measurement_sets": [
{
"@id": "/measurement-sets/IGVFDS0228POXF/",
"accession": "IGVFDS0228POXF",
"aliases": [
"jay-shendure:dev_CRE_mEBs_GEx_repB_10Xlane1_reads"
],
"preferred_assay_title": "MPRA (scQer)",
"status": "released"
}
],
"publications": [
{
"@id": "/publications/398edd7f-1ebb-40a0-a04b-450a2565667c/",
"publication_identifiers": [
"doi:10.1038/s41592-024-02260-3",
"PMID:38724692"
],
"status": "released"
}
],
"release_timestamp": "2024-06-27T00:41:47.366393+00:00",
"samples": [
{
"@id": "/in-vitro-systems/IGVFSM8913GAXO/",
"@type": [
"InVitroSystem",
"Biosample",
"Sample",
"Item"
],
"accession": "IGVFSM8913GAXO",
"aliases": [
"jay-shendure:dev_CRE_mEBs_repB_10Xlane1"
],
"cell_fate_change_treatments": [
"/treatments/9acc7857-c9dd-4b4a-a78b-fdf10c8ae679/"
],
"classifications": [
"differentiated cell specimen"
],
"construct_library_sets": [
"/construct-library-sets/IGVFDS7655GRFI/"
],
"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 21 days (cellular sub pool: 10Xlane1), 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": "12",
"status": "released",
"submitted_by": {
"@id": "/users/73f58e9f-8f5d-4fee-a7cd-dd63c0167e4b/",
"title": "Beth Martin"
},
"submitted_files_timestamp": "2023-12-09T00:58:35.317091+00:00",
"summary": "quantification DNA barcode sequencing for MPRA (scQer) integrating a reporter library targeting accessible genome regions in many genomic loci",
"uuid": "de880773-6e13-440f-a424-21519fc805e2"
}