{
"@context": "/terms/",
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"MeasurementSet",
"FileSet",
"Item"
],
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"jay-shendure:dev_CRE_mEBs_repB_bulk_RNA_day16_reads"
],
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"assay_slims": [
"reporter"
],
"status": "released",
"term_name": "massively parallel reporter assay"
},
"audit": {
"INTERNAL_ACTION": [
{
"category": "missing sequence specification",
"detail": "Auxiliary set [IGVFDS2965JJYR](/auxiliary-sets/IGVFDS2965JJYR/) has sequence file(s): [IGVFFI2907UGPA](/sequence-files/IGVFFI2907UGPA/), [IGVFFI9412XAYU](/sequence-files/IGVFFI9412XAYU/), [IGVFFI4092ZSXR](/sequence-files/IGVFFI4092ZSXR/) which do not have any `seqspecs`. Sequence files in a file set associated with bulk data are expected to link to a sequence specification file.",
"level": 30,
"level_name": "INTERNAL_ACTION",
"name": "audit_missing_seqspec",
"path": "/auxiliary-sets/IGVFDS2965JJYR/"
},
{
"category": "missing sequence specification",
"detail": "Measurement set [IGVFDS9342OPKS](/measurement-sets/IGVFDS9342OPKS/) has sequence file(s): [IGVFFI3026UWXQ](/sequence-files/IGVFFI3026UWXQ/), [IGVFFI6909JPQC](/sequence-files/IGVFFI6909JPQC/), [IGVFFI0572GITJ](/sequence-files/IGVFFI0572GITJ/) which do not have any `seqspecs`. Sequence files in a file set associated with bulk data are expected to link to a sequence specification file.",
"level": 30,
"level_name": "INTERNAL_ACTION",
"name": "audit_missing_seqspec",
"path": "/measurement-sets/IGVFDS9342OPKS/"
}
]
},
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{
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"aliases": [
"jay-shendure:dev_CRE_mEBs_repB_bulk_DNA_day16_reads"
],
"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"
},
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{
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}
],
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"summary": "reporter library targeting accessible genome regions in many genomic loci"
}
],
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"creation_timestamp": "2023-12-08T23:54:06.085739+00:00",
"donors": [
{
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],
"sex": "male",
"status": "released",
"strain_background": "C57BL/6J (B6)",
"taxa": "Mus musculus"
}
],
"externally_hosted": false,
"file_set_type": "experimental data",
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{
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},
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"upload_status": "validated"
},
{
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"creation_timestamp": "2023-12-09T00:56:58.356184+00:00",
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"href": "/sequence-files/IGVFFI3026UWXQ/@@download/IGVFFI3026UWXQ.fastq.gz",
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"status": "released",
"term_name": "Illumina NextSeq 2000"
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},
{
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"controlled_access": false,
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"sequencing_platform": {
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"term_name": "Illumina NextSeq 500"
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"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_repB_d16_RNA_R1_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI6909JPQC/",
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"submitted_file_name": "/net/shendure/vol8/projects/JBL/GEO_sc_rep_fastqs_nobackup/geo_submission_20221108/bulkMPRA_devCRE_mEBs/bulk_MPRA_mEB_series_mBC_repB_d16_RNA_extract_lib_rep_R1_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI0294XRMS/",
"accession": "IGVFFI0294XRMS",
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"jay-shendure:bulkMPRA_devCRE_mEBs_repB_day16_RNA_R2"
],
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"creation_timestamp": "2023-12-09T00:57:00.612009+00:00",
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},
{
"@id": "/sequence-files/IGVFFI0572GITJ/",
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"jay-shendure:bulkMPRA_devCRE_mEBs_repB_day16_RNA_addreads_R2"
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},
{
"@id": "/configuration-files/IGVFFI2592RERK/",
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],
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"status": "in progress",
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"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": [
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],
"publications": [
{
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"PMID:38724692"
],
"status": "released"
}
],
"release_timestamp": "2024-06-27T00:41:14.215057+00:00",
"samples": [
{
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"@type": [
"InVitroSystem",
"Biosample",
"Sample",
"Item"
],
"accession": "IGVFSM8780MGRB",
"aliases": [
"jay-shendure:dev_CRE_mEBs_repB_bulk_day16"
],
"classifications": [
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],
"institutional_certificates": [],
"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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}
],
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"targeted_sample_term": {
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"status": "released",
"term_name": "embryoid body"
},
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}
],
"schema_version": "26",
"status": "released",
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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"
}