{
"@context": "/terms/",
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"@type": [
"MeasurementSet",
"FileSet",
"Item"
],
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"jay-shendure:dev_CRE_mEBs_repB_bulk_RNA_day16_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 [IGVFSM8780MGRB](/in-vitro-systems/IGVFSM8780MGRB/) 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/IGVFSM8780MGRB/"
}
],
"NOT_COMPLIANT": [
{
"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": 50,
"level_name": "NOT_COMPLIANT",
"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": 50,
"level_name": "NOT_COMPLIANT",
"name": "audit_missing_seqspec",
"path": "/auxiliary-sets/IGVFDS2965JJYR/"
}
]
},
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{
"@id": "/auxiliary-sets/IGVFDS2965JJYR/",
"accession": "IGVFDS2965JJYR",
"aliases": [
"jay-shendure:dev_CRE_mEBs_repB_bulk_DNA_day16_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": "2023-12-08T23:54:06.085739+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": [
{
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"accession": "IGVFFI3250EPZQ",
"aliases": [
"jay-shendure:bulkMPRA_devCRE_mEBs_repB_day16_RNA_R3"
],
"content_type": "reads",
"creation_timestamp": "2023-12-09T00:57:01.766819+00:00",
"file_format": "fastq",
"file_size": 380325948,
"href": "/sequence-files/IGVFFI3250EPZQ/@@download/IGVFFI3250EPZQ.fastq.gz",
"s3_uri": "s3://igvf-files/2023/12/09/92fe8705-2715-4ede-896c-5ed02481e148/IGVFFI3250EPZQ.fastq.gz",
"sequencing_platform": {
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"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_repB_d16_RNA_R3_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI3026UWXQ/",
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],
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"creation_timestamp": "2023-12-09T00:56:58.356184+00:00",
"file_format": "fastq",
"file_size": 562155543,
"href": "/sequence-files/IGVFFI3026UWXQ/@@download/IGVFFI3026UWXQ.fastq.gz",
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"sequencing_platform": {
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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_R3_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI3363GMCN/",
"accession": "IGVFFI3363GMCN",
"aliases": [
"jay-shendure:bulkMPRA_devCRE_mEBs_repB_day16_RNA_R1"
],
"content_type": "reads",
"creation_timestamp": "2023-12-09T00:56:59.440826+00:00",
"file_format": "fastq",
"file_size": 261508957,
"href": "/sequence-files/IGVFFI3363GMCN/@@download/IGVFFI3363GMCN.fastq.gz",
"s3_uri": "s3://igvf-files/2023/12/09/66c821e5-8ea0-4ad7-aa3a-ebf410f0cb80/IGVFFI3363GMCN.fastq.gz",
"sequencing_platform": {
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"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_repB_d16_RNA_R1_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI6909JPQC/",
"accession": "IGVFFI6909JPQC",
"aliases": [
"jay-shendure:bulkMPRA_devCRE_mEBs_repB_day16_RNA_addreads_R1"
],
"content_type": "reads",
"creation_timestamp": "2023-12-09T00:56:55.733459+00:00",
"file_format": "fastq",
"file_size": 551011612,
"href": "/sequence-files/IGVFFI6909JPQC/@@download/IGVFFI6909JPQC.fastq.gz",
"s3_uri": "s3://igvf-files/2023/12/09/076cd2ac-8e38-459e-807a-ec7883ea61ff/IGVFFI6909JPQC.fastq.gz",
"sequencing_platform": {
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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",
"aliases": [
"jay-shendure:bulkMPRA_devCRE_mEBs_repB_day16_RNA_R2"
],
"content_type": "reads",
"creation_timestamp": "2023-12-09T00:57:00.612009+00:00",
"file_format": "fastq",
"file_size": 131387771,
"href": "/sequence-files/IGVFFI0294XRMS/@@download/IGVFFI0294XRMS.fastq.gz",
"s3_uri": "s3://igvf-files/2023/12/09/4e17138e-4649-41b5-87ff-2133923aa07c/IGVFFI0294XRMS.fastq.gz",
"sequencing_platform": {
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"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_repB_d16_RNA_R2_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI0572GITJ/",
"accession": "IGVFFI0572GITJ",
"aliases": [
"jay-shendure:bulkMPRA_devCRE_mEBs_repB_day16_RNA_addreads_R2"
],
"content_type": "reads",
"creation_timestamp": "2023-12-09T00:56:57.081267+00:00",
"file_format": "fastq",
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"href": "/sequence-files/IGVFFI0572GITJ/@@download/IGVFFI0572GITJ.fastq.gz",
"s3_uri": "s3://igvf-files/2023/12/09/59ec0c1c-18fa-4996-8cad-b3a01dacf195/IGVFFI0572GITJ.fastq.gz",
"sequencing_platform": {
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"term_name": "Illumina NextSeq 2000"
},
"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_R2_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": "2024-06-27T00:41:14.215057+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",
"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 induced to embryoid body for 16 days, 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": "2023-12-09T00:56:47.248153+00:00",
"summary": "MPRA integrating a reporter library targeting accessible genome regions in many genomic loci",
"uuid": "8eaa35a3-a597-4631-9919-589561efbada"
}