{
"@context": "/terms/",
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"MeasurementSet",
"FileSet",
"Item"
],
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"aliases": [
"jay-shendure:dev_CRE_mEBs_GEx_repA_10Xlane1_reads"
],
"assay_term": {
"@id": "/assay-terms/NTR_000789/",
"assay_slims": [
"no category"
],
"status": "released",
"term_name": "single cell massively parallel reporter assay"
},
"audit": {
"INTERNAL_ACTION": [
{
"category": "unexpected seqspecs",
"detail": "Sequence File [IGVFFI9161RRDV](/sequence-files/IGVFFI9161RRDV/) has multiple in progress sequence specification files. A sequence file is expected to have only one in progress sequence specification file.",
"level": 30,
"level_name": "INTERNAL_ACTION",
"name": "audit_multiple_seqspec_per_seqfile",
"path": "/sequence-files/IGVFFI9161RRDV/"
},
{
"category": "unexpected seqspecs",
"detail": "Sequence File [IGVFFI5772LMXH](/sequence-files/IGVFFI5772LMXH/) has multiple in progress sequence specification files. A sequence file is expected to have only one in progress sequence specification file.",
"level": 30,
"level_name": "INTERNAL_ACTION",
"name": "audit_multiple_seqspec_per_seqfile",
"path": "/sequence-files/IGVFFI5772LMXH/"
},
{
"category": "unexpected seqspecs",
"detail": "Sequence File [IGVFFI8739CFNW](/sequence-files/IGVFFI8739CFNW/) has multiple in progress sequence specification files. A sequence file is expected to have only one in progress sequence specification file.",
"level": 30,
"level_name": "INTERNAL_ACTION",
"name": "audit_multiple_seqspec_per_seqfile",
"path": "/sequence-files/IGVFFI8739CFNW/"
},
{
"category": "NTR term ID",
"detail": "Assay term for [NTR_000789](/assay-terms/NTR_000789/) has been newly requested. Ontology terms with a newly requested term ID are expected to have it updated following its addition to the appropriate ontology database.",
"level": 30,
"level_name": "INTERNAL_ACTION",
"name": "audit_ntr_term_id",
"path": "/assay-terms/NTR_000789/"
}
]
},
"auxiliary_sets": [
{
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"accession": "IGVFDS5801KSAS",
"aliases": [
"jay-shendure:dev_CRE_mEBs_mBC_repA_10Xlane1_reads"
],
"file_set_type": "quantification DNA barcode sequencing",
"status": "released"
},
{
"@id": "/auxiliary-sets/IGVFDS7792HFAY/",
"accession": "IGVFDS7792HFAY",
"aliases": [
"jay-shendure:dev_CRE_mEBs_oBC_repA_10Xlane1_reads"
],
"file_set_type": "circularized RNA barcode detection",
"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"
},
"construct_library_sets": [
{
"@id": "/construct-library-sets/IGVFDS7655GRFI/",
"accession": "IGVFDS7655GRFI",
"file_set_type": "reporter library",
"integrated_content_files": [
{
"@id": "/tabular-files/IGVFFI8904VCYX/",
"accession": "IGVFFI8904VCYX",
"content_type": "MPRA sequence designs",
"status": "released",
"summary": "MPRA sequence designs"
}
],
"status": "released",
"summary": "reporter library targeting accessible genome regions in many genomic loci"
}
],
"control_for": [],
"creation_timestamp": "2023-12-08T23:53:46.743065+00:00",
"donors": [
{
"@id": "/rodent-donors/IGVFDO3898MNLZ/",
"accession": "IGVFDO3898MNLZ",
"aliases": [
"jay-shendure:WD44_donor"
],
"sex": "male",
"status": "released",
"strain_background": "C57BL/6J (B6)",
"taxa": "Mus musculus"
}
],
"externally_hosted": false,
"file_set_type": "experimental data",
"files": [
{
"@id": "/sequence-files/IGVFFI8739CFNW/",
"accession": "IGVFFI8739CFNW",
"aliases": [
"jay-shendure:sc_rep_devCRE_mEBs_GEx_repA_10Xlane1_I1"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2023-12-09T00:58:07.059552+00:00",
"file_format": "fastq",
"file_size": 395407505,
"href": "/sequence-files/IGVFFI8739CFNW/@@download/IGVFFI8739CFNW.fastq.gz",
"s3_uri": "s3://igvf-files/2023/12/09/96f782b1-5d24-490c-ad8b-2d88e1dee903/IGVFFI8739CFNW.fastq.gz",
"sequencing_platform": {
"@id": "/platform-terms/EFO_0009173/",
"status": "released",
"term_name": "Illumina NextSeq 500"
},
"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_GEx_repA_lane1_I1_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI5772LMXH/",
"accession": "IGVFFI5772LMXH",
"aliases": [
"jay-shendure:sc_rep_devCRE_mEBs_GEx_repA_10Xlane1_R1"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2023-12-09T00:58:08.214125+00:00",
"file_format": "fastq",
"file_size": 1165897765,
"href": "/sequence-files/IGVFFI5772LMXH/@@download/IGVFFI5772LMXH.fastq.gz",
"s3_uri": "s3://igvf-files/2023/12/09/06ea30e2-f6b5-40dd-b13e-aef9e87c8b58/IGVFFI5772LMXH.fastq.gz",
"sequencing_platform": {
"@id": "/platform-terms/EFO_0009173/",
"status": "released",
"term_name": "Illumina NextSeq 500"
},
"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_GEx_repA_lane1_R1_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI9161RRDV/",
"accession": "IGVFFI9161RRDV",
"aliases": [
"jay-shendure:sc_rep_devCRE_mEBs_GEx_repA_10Xlane1_R2"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2023-12-09T00:58:09.308750+00:00",
"file_format": "fastq",
"file_size": 1860772006,
"href": "/sequence-files/IGVFFI9161RRDV/@@download/IGVFFI9161RRDV.fastq.gz",
"s3_uri": "s3://igvf-files/2023/12/09/52d7c69e-95a1-4379-a720-fffd19044966/IGVFFI9161RRDV.fastq.gz",
"sequencing_platform": {
"@id": "/platform-terms/EFO_0009173/",
"status": "released",
"term_name": "Illumina NextSeq 500"
},
"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_GEx_repA_lane1_R2_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/configuration-files/IGVFFI1829MGSH/",
"accession": "IGVFFI1829MGSH",
"aliases": [
"jay-shendure:old_seqspec_of_set_IGVFDS5248DHZT"
],
"content_type": "seqspec",
"creation_timestamp": "2024-08-22T22:51:06.744269+00:00",
"file_format": "yaml",
"file_size": 829,
"href": "/configuration-files/IGVFFI1829MGSH/@@download/IGVFFI1829MGSH.yaml.gz",
"s3_uri": "s3://igvf-files/2024/08/22/5b658ad6-2e6e-4348-a87b-057a2e9e4f7e/IGVFFI1829MGSH.yaml.gz",
"status": "in progress",
"submitted_file_name": "/net/shendure/vol1/home/martin91/IGVF/forupload/seqspecs/scQers/scQers_IGVFDS5248DHZT_seqspec.yaml.gz",
"upload_status": "validated"
},
{
"@id": "/configuration-files/IGVFFI7183UWAG/",
"accession": "IGVFFI7183UWAG",
"aliases": [
"jay-shendure:seqspec_of_set_IGVFDS5248DHZT"
],
"content_type": "seqspec",
"creation_timestamp": "2025-03-24T19:35:11.745748+00:00",
"file_format": "yaml",
"file_size": 1223,
"href": "/configuration-files/IGVFFI7183UWAG/@@download/IGVFFI7183UWAG.yaml.gz",
"s3_uri": "s3://igvf-files/2025/03/24/1a52e42e-0458-4f6d-b1f8-2b510e9a3500/IGVFFI7183UWAG.yaml.gz",
"status": "in progress",
"submitted_file_name": "/net/shendure/vol1/home/martin91/IGVF/forupload/seqspecs/scQers/scQers_IGVFDS5248DHZT_GEx_seqspec_v3.yaml.gz",
"upload_status": "validated"
}
],
"input_for": [
"/analysis-sets/IGVFDS2774OLAH/"
],
"lab": {
"@id": "/labs/jay-shendure/",
"title": "Jay Shendure, UW"
},
"notes": "The readout 86015c12-b9a6-43ba-9601-5d75aab4d39c was removed from this measurement set.",
"preferred_assay_title": "MPRA (scQer)",
"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": "2024-06-27T00:41:46.650330+00:00",
"samples": [
{
"@id": "/in-vitro-systems/IGVFSM4494VUEQ/",
"@type": [
"InVitroSystem",
"Biosample",
"Sample",
"Item"
],
"accession": "IGVFSM4494VUEQ",
"aliases": [
"jay-shendure:dev_CRE_mEBs_repA_10Xlane1"
],
"cellular_sub_pool": "10Xlane1",
"classifications": [
"differentiated cell specimen"
],
"institutional_certificates": [],
"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": "Mus musculus WD44 (male) mouse embryonic stem differentiated cell specimen induced to embryoid body for 21 days (cellular sub pool: 10Xlane1) transfected with a reporter library",
"targeted_sample_term": {
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"status": "released",
"term_name": "embryoid body"
},
"taxa": "Mus musculus"
}
],
"schema_version": "26",
"status": "released",
"submitted_by": {
"@id": "/users/73f58e9f-8f5d-4fee-a7cd-dd63c0167e4b/",
"title": "Beth Martin"
},
"submitted_files_timestamp": "2023-12-09T00:58:07.059552+00:00",
"summary": "MPRA (scQer) integrating a reporter library targeting accessible genome regions in many genomic loci",
"uuid": "575ddf6b-2fad-4b0d-8ee7-88f64faf0a05"
}