{
"@context": "/terms/",
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"MeasurementSet",
"FileSet",
"Item"
],
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],
"assay_term": {
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"status": "released",
"term_name": "massively parallel reporter assay"
},
"audit": {
"INTERNAL_ACTION": [
{
"category": "missing sequence specification",
"detail": "Measurement set [IGVFDS9342OPKS](/measurement-sets/IGVFDS9342OPKS/) has sequence file(s): [IGVFFI3250EPZQ](/sequence-files/IGVFFI3250EPZQ/), [IGVFFI3026UWXQ](/sequence-files/IGVFFI3026UWXQ/), [IGVFFI3363GMCN](/sequence-files/IGVFFI3363GMCN/), [IGVFFI6909JPQC](/sequence-files/IGVFFI6909JPQC/), [IGVFFI0294XRMS](/sequence-files/IGVFFI0294XRMS/), [IGVFFI0572GITJ](/sequence-files/IGVFFI0572GITJ/) 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/IGVFDS9342OPKS/"
},
{
"category": "missing sequence specification",
"detail": "Auxiliary set [IGVFDS2965JJYR](/auxiliary-sets/IGVFDS2965JJYR/) has sequence file(s): [IGVFFI2907UGPA](/sequence-files/IGVFFI2907UGPA/), [IGVFFI2511SPLG](/sequence-files/IGVFFI2511SPLG/), [IGVFFI2927UCHR](/sequence-files/IGVFFI2927UCHR/), [IGVFFI9412XAYU](/sequence-files/IGVFFI9412XAYU/), [IGVFFI4092ZSXR](/sequence-files/IGVFFI4092ZSXR/), [IGVFFI5253XKCX](/sequence-files/IGVFFI5253XKCX/) 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/IGVFDS2965JJYR/"
}
]
},
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{
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],
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}
],
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"title": "Jay Shendure"
},
"title": "Massively parallel characterization of variants and elements impacting transcriptional regulation in dynamic cellular systems"
},
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"creation_timestamp": "2023-12-08T23:54:06.085739+00:00",
"donors": [
{
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"accession": "IGVFDO3898MNLZ",
"aliases": [
"jay-shendure:WD44_donor"
],
"sex": "male",
"status": "released",
"taxa": "Mus musculus"
}
],
"externally_hosted": false,
"file_set_type": "experimental data",
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{
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"term_name": "Illumina NextSeq 500"
},
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},
{
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"status": "released",
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},
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"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI3363GMCN/",
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"aliases": [
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"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2023-12-09T00:56:59.440826+00:00",
"file_format": "fastq",
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"href": "/sequence-files/IGVFFI3363GMCN/@@download/IGVFFI3363GMCN.fastq.gz",
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"term_name": "Illumina NextSeq 500"
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"upload_status": "validated"
},
{
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"creation_timestamp": "2023-12-09T00:56:55.733459+00:00",
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"href": "/sequence-files/IGVFFI6909JPQC/@@download/IGVFFI6909JPQC.fastq.gz",
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},
{
"@id": "/sequence-files/IGVFFI0294XRMS/",
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"jay-shendure:bulkMPRA_devCRE_mEBs_repB_day16_RNA_R2"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2023-12-09T00:57:00.612009+00:00",
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{
"@id": "/sequence-files/IGVFFI0572GITJ/",
"accession": "IGVFFI0572GITJ",
"aliases": [
"jay-shendure:bulkMPRA_devCRE_mEBs_repB_day16_RNA_addreads_R2"
],
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}
],
"input_for": [
"/analysis-sets/IGVFDS2622CKLA/"
],
"lab": {
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"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": [
{
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"PMID:38724692"
],
"status": "released"
}
],
"release_timestamp": "2024-06-27T00:41:14.215057+00:00",
"samples": [
{
"@id": "/in-vitro-systems/IGVFSM8780MGRB/",
"@type": [
"InVitroSystem",
"Biosample",
"Sample",
"Item"
],
"accession": "IGVFSM8780MGRB",
"aliases": [
"jay-shendure:dev_CRE_mEBs_repB_bulk_day16"
],
"cell_fate_change_treatments": [
{
"@id": "/treatments/9acc7857-c9dd-4b4a-a78b-fdf10c8ae679/",
"purpose": "differentiation",
"status": "released",
"summary": "Depletion of Leukemia inhibitory factor",
"treatment_type": "protein"
}
],
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"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": [
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"OntologyTerm",
"Item"
],
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"summary": "mouse embryonic stem cell",
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}
],
"status": "released",
"summary": "mouse embryonic stem differentiated cell specimen induced to embryoid body for 16 days, male, Mus musculus WD44 transfected with a reporter library",
"targeted_sample_term": {
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"status": "released",
"term_name": "embryoid body"
},
"taxa": "Mus musculus"
}
],
"schema_version": "23",
"status": "released",
"submitted_by": {
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"title": "Beth Martin"
},
"submitted_files_timestamp": "2023-12-09T00:56:47.248153+00:00",
"summary": "MPRA integrating a reporter library targeting accessible genome regions in many genomic loci",
"uuid": "8eaa35a3-a597-4631-9919-589561efbada"
}