{
"@context": "/terms/",
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"FileSet",
"Item"
],
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],
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"status": "released",
"term_name": "massively parallel reporter assay"
},
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"INTERNAL_ACTION": [
{
"category": "missing sequence specification",
"detail": "Auxiliary set [IGVFDS1491XCOB](/auxiliary-sets/IGVFDS1491XCOB/) has sequence file(s): [IGVFFI1497OPGZ](/sequence-files/IGVFFI1497OPGZ/), [IGVFFI3440QHAY](/sequence-files/IGVFFI3440QHAY/), [IGVFFI3452FMVQ](/sequence-files/IGVFFI3452FMVQ/) 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/IGVFDS1491XCOB/"
},
{
"category": "missing sequence specification",
"detail": "Measurement set [IGVFDS8101YKZJ](/measurement-sets/IGVFDS8101YKZJ/) has sequence file(s): [IGVFFI6760IVRH](/sequence-files/IGVFFI6760IVRH/), [IGVFFI0333NSOF](/sequence-files/IGVFFI0333NSOF/), [IGVFFI1477RYGS](/sequence-files/IGVFFI1477RYGS/) 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/IGVFDS8101YKZJ/"
}
]
},
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{
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],
"file_set_type": "quantification DNA barcode sequencing",
"status": "released"
}
],
"award": {
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"component": "functional characterization",
"contact_pi": {
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"title": "Jay Shendure"
},
"title": "Massively parallel characterization of variants and elements impacting transcriptional regulation in dynamic cellular systems"
},
"control_for": [],
"creation_timestamp": "2023-12-08T23:53:51.083935+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": [
{
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"accession": "IGVFFI6760IVRH",
"aliases": [
"jay-shendure:bulkMPRA_devCRE_mEBs_repA_day0_RNA_R1"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2023-12-09T00:54:08.582135+00:00",
"file_format": "fastq",
"file_size": 453358265,
"href": "/sequence-files/IGVFFI6760IVRH/@@download/IGVFFI6760IVRH.fastq.gz",
"s3_uri": "s3://igvf-files/2023/12/09/54d257b8-72cc-4af9-a6f7-d3b5db225567/IGVFFI6760IVRH.fastq.gz",
"sequencing_platform": {
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"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/bulkMPRA_devCRE_mEBs/bulk_MPRA_mEB_series_mBC_repA_d00_RNA_R1_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI0333NSOF/",
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"aliases": [
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],
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"controlled_access": false,
"creation_timestamp": "2023-12-09T00:54:10.979161+00:00",
"file_format": "fastq",
"file_size": 654549966,
"href": "/sequence-files/IGVFFI0333NSOF/@@download/IGVFFI0333NSOF.fastq.gz",
"s3_uri": "s3://igvf-files/2023/12/09/a8f91617-5f2c-4170-bf63-bc60991f4359/IGVFFI0333NSOF.fastq.gz",
"sequencing_platform": {
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"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/bulkMPRA_devCRE_mEBs/bulk_MPRA_mEB_series_mBC_repA_d00_RNA_R3_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI1477RYGS/",
"accession": "IGVFFI1477RYGS",
"aliases": [
"jay-shendure:bulkMPRA_devCRE_mEBs_repA_day0_RNA_R2"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2023-12-09T00:54:09.816416+00:00",
"file_format": "fastq",
"file_size": 221708005,
"href": "/sequence-files/IGVFFI1477RYGS/@@download/IGVFFI1477RYGS.fastq.gz",
"s3_uri": "s3://igvf-files/2023/12/09/3a180b33-ddc9-45f3-94ac-dcdf07ba8138/IGVFFI1477RYGS.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/bulkMPRA_devCRE_mEBs/bulk_MPRA_mEB_series_mBC_repA_d00_RNA_R2_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": "2024-06-27T00:41:18.910059+00:00",
"samples": [
{
"@id": "/in-vitro-systems/IGVFSM0716YPPC/",
"@type": [
"InVitroSystem",
"Biosample",
"Sample",
"Item"
],
"accession": "IGVFSM0716YPPC",
"aliases": [
"jay-shendure:dev_CRE_mEBs_repA_bulk_day0"
],
"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, 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": "2023-12-09T00:54:05.014487+00:00",
"summary": "MPRA integrating a reporter library targeting accessible genome regions in many genomic loci",
"uuid": "7f0df8ed-26d4-48e0-b927-8b414d46c1bc"
}