{
"@context": "/terms/",
"@id": "/auxiliary-sets/IGVFDS2360YYBI/",
"@type": [
"AuxiliarySet",
"FileSet",
"Item"
],
"accession": "IGVFDS2360YYBI",
"aliases": [
"jesse-engreitz:auxiliary_set_eRZ10_teloHAEC_TLNRD1_enhancer_CRISPRi_FlowFISH_Rep4_bin1"
],
"audit": {
"INTERNAL_ACTION": [
{
"category": "mismatched status",
"detail": "Released auxiliary set [IGVFDS2360YYBI](/auxiliary-sets/IGVFDS2360YYBI/) has in progress subobject publication [2e37380f-fb50-4dbc-a7ec-e9e6532c9f99](/publications/2e37380f-fb50-4dbc-a7ec-e9e6532c9f99/).",
"level": 30,
"level_name": "INTERNAL_ACTION",
"name": "audit_item_status",
"path": "/auxiliary-sets/IGVFDS2360YYBI/"
},
{
"category": "NTR term ID",
"detail": "Sample term for [NTR_0000753](/sample-terms/NTR_0000753/) has been newly requested. Ontology terms with a newly requested term ID are expected to have it updated following its addition to the appropriate ontology database.",
"level": 30,
"level_name": "INTERNAL_ACTION",
"name": "audit_ntr_term_id",
"path": "/sample-terms/NTR_0000753/"
}
],
"NOT_COMPLIANT": [
{
"category": "missing sequence specification",
"detail": "Auxiliary set [IGVFDS2360YYBI](/auxiliary-sets/IGVFDS2360YYBI/) has sequence file(s): [IGVFFI7086QPVW](/sequence-files/IGVFFI7086QPVW/) 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/IGVFDS2360YYBI/"
}
],
"WARNING": [
{
"category": "missing sequencing kit",
"detail": "Auxiliary set [IGVFDS2360YYBI](/auxiliary-sets/IGVFDS2360YYBI/) has sequence file(s) [IGVFFI7086QPVW](/sequence-files/IGVFFI7086QPVW/) which lack specification of a `sequencing_kit`. Sequence files should specify a sequencing kit.",
"level": 40,
"level_name": "WARNING",
"name": "audit_inconsistent_sequencing_kit",
"path": "/auxiliary-sets/IGVFDS2360YYBI/"
}
]
},
"award": {
"@id": "/awards/HG011972/",
"component": "functional characterization",
"contact_pi": {
"@id": "/users/6c75dbfa-635e-4a7a-8ec8-9e51e9c380a4/",
"title": "Jesse Engreitz"
},
"title": "Stanford Center for Connecting DNA Variants to Function and Phenotype"
},
"control_for": [],
"creation_timestamp": "2024-06-27T17:41:56.770159+00:00",
"donors": [
{
"@id": "/human-donors/IGVFDO3459DFTW/",
"accession": "IGVFDO3459DFTW",
"aliases": [
"igvf:donor_of_teloHAEC"
],
"sex": "female",
"status": "released",
"taxa": "Homo sapiens"
}
],
"file_set_type": "gRNA sequencing",
"files": [
{
"@id": "/sequence-files/IGVFFI7086QPVW/",
"accession": "IGVFFI7086QPVW",
"aliases": [
"jesse-engreitz:sequence_data_eRZ10_teloHAEC_TLNRD1_enhancer_CRISPRi_FlowFISH_Rep4_bin1"
],
"content_type": "reads",
"creation_timestamp": "2023-12-05T00:48:28.380916+00:00",
"file_format": "fastq",
"file_size": 91571340,
"href": "/sequence-files/IGVFFI7086QPVW/@@download/IGVFFI7086QPVW.fastq.gz",
"s3_uri": "s3://igvf-files/2023/12/05/4c0e9b65-c8ee-469a-a749-13358d81dde4/IGVFFI7086QPVW.fastq.gz",
"sequencing_platform": "/platform-terms/EFO_0008566/",
"submitted_file_name": "/Users/ronghao/Desktop/Research/data/eRZ10_FlowFISH/TLNRD1/eRZ10_FlowFISH_fastq/T4_bin1_S31_R1_001.fastq.gz",
"upload_status": "validated"
}
],
"input_file_set_for": [
"/analysis-sets/IGVFDS9053MHCS/"
],
"lab": {
"@id": "/labs/jesse-engreitz/",
"title": "Jesse Engreitz, Stanford"
},
"measurement_sets": [
{
"@id": "/measurement-sets/IGVFDS1890YDYU/",
"accession": "IGVFDS1890YDYU",
"aliases": [
"jesse-engreitz:measurement_set_eRZ10_teloHAEC_TLNRD1_enhancer_CRISPRi_FlowFISH_Rep4_bin1"
],
"preferred_assay_title": "CRISPR FlowFISH screen"
}
],
"publications": [
{
"@id": "/publications/2e37380f-fb50-4dbc-a7ec-e9e6532c9f99/",
"publication_identifiers": [
"PMID:38326615"
]
}
],
"release_timestamp": "2024-06-27T17:53:02.041561+00:00",
"samples": [
{
"@id": "/in-vitro-systems/IGVFSM0599MHTG/",
"@type": [
"InVitroSystem",
"Biosample",
"Sample",
"Item"
],
"accession": "IGVFSM0599MHTG",
"aliases": [
"jesse-engreitz:in-vitro-system_eRZ10_teloHAEC_TLNRD1_enhancer_CRISPRi_FlowFISH_Rep4_bin1"
],
"classifications": [
"cell line"
],
"construct_library_sets": [
"/construct-library-sets/IGVFDS7621RRLM/"
],
"modifications": [
"/crispr-modifications/b4bc725a-8eeb-4180-9789-bece3516c0c1/"
],
"sample_terms": [
{
"@id": "/sample-terms/NTR_0000753/",
"@type": [
"SampleTerm",
"OntologyTerm",
"Item"
],
"aliases": [
"igvf:TeloHAEC"
],
"status": "released",
"summary": "TeloHAEC",
"term_name": "TeloHAEC"
}
],
"status": "released",
"summary": "TeloHAEC cell line, female, Homo sapiens (sorting details: FACS bin for 0-25% expression of TLNRD1) modified with a guide library",
"taxa": "Homo sapiens"
}
],
"schema_version": "11",
"status": "released",
"submitted_by": {
"@id": "/users/1e75d989-a438-4d77-a451-8a297fd3636e/",
"title": "Ian Whaling"
},
"submitted_files_timestamp": "2023-12-05T00:48:28.380916+00:00",
"summary": "gRNA sequencing for CRISPR interference FlowFISH screen integrating a guide (sgRNA) library targeting candidate cis-regulatory elements in a genomic locus",
"uuid": "4255653f-62a0-48e5-bc26-6e6afb2cb65b"
}