{
"@context": "/terms/",
"@id": "/measurement-sets/IGVFDS2047KEEM/",
"@type": [
"MeasurementSet",
"FileSet",
"Item"
],
"accession": "IGVFDS2047KEEM",
"aliases": [
"jay-shendure:dev_CRE_mEBs_rep2B_part2_bulk_RNA_day0_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 [IGVFSM5495EAGK](/in-vitro-systems/IGVFSM5495EAGK/) 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/IGVFSM5495EAGK/"
}
],
"NOT_COMPLIANT": [
{
"category": "missing sequence specification",
"detail": "Measurement set [IGVFDS2047KEEM](/measurement-sets/IGVFDS2047KEEM/) has sequence file(s): [IGVFFI9843VEFQ](/sequence-files/IGVFFI9843VEFQ/), [IGVFFI6751XIUR](/sequence-files/IGVFFI6751XIUR/), [IGVFFI1523TEYV](/sequence-files/IGVFFI1523TEYV/) 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/IGVFDS2047KEEM/"
},
{
"category": "missing sequence specification",
"detail": "Auxiliary set [IGVFDS4218HPCH](/auxiliary-sets/IGVFDS4218HPCH/) has sequence file(s): [IGVFFI8548MIAL](/sequence-files/IGVFFI8548MIAL/), [IGVFFI0006GAWG](/sequence-files/IGVFFI0006GAWG/), [IGVFFI4306WJSO](/sequence-files/IGVFFI4306WJSO/) 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/IGVFDS4218HPCH/"
}
]
},
"auxiliary_sets": [
{
"@id": "/auxiliary-sets/IGVFDS4218HPCH/",
"accession": "IGVFDS4218HPCH",
"aliases": [
"jay-shendure:dev_CRE_mEBs_rep2B_part2_bulk_DNA_day0_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": "2023-12-08T23:54:15.283049+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/IGVFFI9843VEFQ/",
"accession": "IGVFFI9843VEFQ",
"aliases": [
"jay-shendure:bulkMPRA_devCRE_mEBs_rep2B_2_day0_RNA_R2"
],
"content_type": "reads",
"creation_timestamp": "2023-12-09T00:53:12.817455+00:00",
"file_format": "fastq",
"file_size": 255505669,
"href": "/sequence-files/IGVFFI9843VEFQ/@@download/IGVFFI9843VEFQ.fastq.gz",
"s3_uri": "s3://igvf-files/2023/12/09/70df2e03-23d3-4e51-9498-66f89944ff9e/IGVFFI9843VEFQ.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_rep2B2_d00_RNA_R2_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI6751XIUR/",
"accession": "IGVFFI6751XIUR",
"aliases": [
"jay-shendure:bulkMPRA_devCRE_mEBs_rep2B_2_day0_RNA_R3"
],
"content_type": "reads",
"creation_timestamp": "2023-12-09T00:53:14.052624+00:00",
"file_format": "fastq",
"file_size": 303666349,
"href": "/sequence-files/IGVFFI6751XIUR/@@download/IGVFFI6751XIUR.fastq.gz",
"s3_uri": "s3://igvf-files/2023/12/09/276dbf0e-cec7-42ba-9cc9-14d357b77ec0/IGVFFI6751XIUR.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_rep2B2_d00_RNA_R3_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI1523TEYV/",
"accession": "IGVFFI1523TEYV",
"aliases": [
"jay-shendure:bulkMPRA_devCRE_mEBs_rep2B_2_day0_RNA_R1"
],
"content_type": "reads",
"creation_timestamp": "2023-12-09T00:53:11.679585+00:00",
"file_format": "fastq",
"file_size": 273516650,
"href": "/sequence-files/IGVFFI1523TEYV/@@download/IGVFFI1523TEYV.fastq.gz",
"s3_uri": "s3://igvf-files/2023/12/09/048c04f3-434a-49c7-a72e-c40ca6a06bab/IGVFFI1523TEYV.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_rep2B2_d00_RNA_R1_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": "2024-06-27T00:41:19.309359+00:00",
"samples": [
{
"@id": "/in-vitro-systems/IGVFSM5495EAGK/",
"@type": [
"InVitroSystem",
"Biosample",
"Sample",
"Item"
],
"accession": "IGVFSM5495EAGK",
"aliases": [
"jay-shendure:dev_CRE_mEBs_rep2B_part2_bulk_day0"
],
"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, 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": "2023-12-09T00:53:07.624149+00:00",
"summary": "MPRA integrating a reporter library targeting accessible genome regions in many genomic loci",
"uuid": "0e0a07c8-793a-4ed4-b8f8-fe40ae341656"
}