{
"@context": "/terms/",
"@id": "/auxiliary-sets/IGVFDS5772WTGS/",
"@type": [
"AuxiliarySet",
"FileSet",
"Item"
],
"accession": "IGVFDS5772WTGS",
"aliases": [
"jesse-engreitz:auxiliary_CRUDO_FAM3C_Auxin6hrs-FF1-BinF-PCR1-Rep1_S138",
"jesse-engreitz:auxiliary_CRUDO_FAM3C_Auxin6hrs-FF1-BinF-PCR2-Rep1_S144",
"jesse-engreitz:auxiliary_CRUDO_FAM3C_Auxin6hrs-FF1-BinF-PCR3-Rep1_S192",
"jesse-engreitz:auxiliary_CRUDO_FAM3C_Auxin6hrs-FF1-BinF-PCR4-Rep1_S198"
],
"audit": {
"INTERNAL_ACTION": [
{
"category": "missing sequencing kit",
"detail": "Auxiliary set [IGVFDS5772WTGS](/auxiliary-sets/IGVFDS5772WTGS/) has sequence file(s) [IGVFFI9374WFBZ](/sequence-files/IGVFFI9374WFBZ/), [IGVFFI7816MRXM](/sequence-files/IGVFFI7816MRXM/), [IGVFFI1752SCWZ](/sequence-files/IGVFFI1752SCWZ/), [IGVFFI3818YHBA](/sequence-files/IGVFFI3818YHBA/) which lack specification of a `sequencing_kit`. Sequence files should specify a sequencing kit.",
"level": 30,
"level_name": "INTERNAL_ACTION",
"name": "audit_inconsistent_sequencing_kit",
"path": "/auxiliary-sets/IGVFDS5772WTGS/"
}
]
},
"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": "2024-05-14T16:51:12.631305+00:00",
"donors": [
{
"@id": "/human-donors/IGVFDO0384OZRW/",
"accession": "IGVFDO0384OZRW",
"aliases": [
"igvf:donor_of_HCT116"
],
"sex": "male",
"status": "released",
"taxa": "Homo sapiens"
}
],
"file_set_type": "gRNA sequencing",
"files": [
{
"@id": "/sequence-files/IGVFFI9374WFBZ/",
"accession": "IGVFFI9374WFBZ",
"aliases": [
"jesse-engreitz:auxiliary_file_CRUDO_FAM3C_Auxin6hrs-FF1-BinF-PCR1-Rep1_S138"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2024-06-01T01:53:34.859990+00:00",
"file_format": "fastq",
"file_size": 28163239,
"href": "/sequence-files/IGVFFI9374WFBZ/@@download/IGVFFI9374WFBZ.fastq.gz",
"s3_uri": "s3://igvf-files/2024/06/01/225ff9a4-28e1-4528-9531-4e776bd7ab34/IGVFFI9374WFBZ.fastq.gz",
"sequencing_platform": "/platform-terms/EFO_0008565/",
"status": "released",
"submitted_file_name": "/oak/stanford/groups/engreitz/Projects/Cohesin/220308B014_CCND1_SSFA2_FAM3C/fastq_trim/FAM3C-Auxin6hrs-FF1-BinF-PCR1-Rep1_S138_R1_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/configuration-files/IGVFFI7297AXPH/",
"accession": "IGVFFI7297AXPH",
"aliases": [
"jesse-engreitz:seqspecfile_CRUDO_FAM3C_Auxin6hrs-FF1-BinF-PCR1-Rep1_S138"
],
"content_type": "seqspec",
"creation_timestamp": "2024-06-11T20:43:53.179370+00:00",
"file_format": "yaml",
"file_size": 915,
"href": "/configuration-files/IGVFFI7297AXPH/@@download/IGVFFI7297AXPH.yaml.gz",
"s3_uri": "s3://igvf-files/2024/06/11/e1ec87eb-050f-4ece-9111-8414c0918e04/IGVFFI7297AXPH.yaml.gz",
"status": "released",
"submitted_file_name": "/oak/stanford/groups/engreitz/Projects/Cohesin/240410_IGVF_upload/seqspec/guideseq.out.FAM3C_Auxin6hrs-FF1-BinF-PCR1-Rep1_S138.yaml",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI7816MRXM/",
"accession": "IGVFFI7816MRXM",
"aliases": [
"jesse-engreitz:auxiliary_file_CRUDO_FAM3C_Auxin6hrs-FF1-BinF-PCR2-Rep1_S144"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2024-06-01T01:53:53.150402+00:00",
"file_format": "fastq",
"file_size": 24050486,
"href": "/sequence-files/IGVFFI7816MRXM/@@download/IGVFFI7816MRXM.fastq.gz",
"s3_uri": "s3://igvf-files/2024/06/01/7aff82f3-ee66-4bdf-9fd7-ce0a3eb7cc8b/IGVFFI7816MRXM.fastq.gz",
"sequencing_platform": "/platform-terms/EFO_0008565/",
"status": "released",
"submitted_file_name": "/oak/stanford/groups/engreitz/Projects/Cohesin/220308B014_CCND1_SSFA2_FAM3C/fastq_trim/FAM3C-Auxin6hrs-FF1-BinF-PCR2-Rep1_S144_R1_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI1752SCWZ/",
"accession": "IGVFFI1752SCWZ",
"aliases": [
"jesse-engreitz:auxiliary_file_CRUDO_FAM3C_Auxin6hrs-FF1-BinF-PCR4-Rep1_S198"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2024-06-01T01:54:30.207058+00:00",
"file_format": "fastq",
"file_size": 32574355,
"href": "/sequence-files/IGVFFI1752SCWZ/@@download/IGVFFI1752SCWZ.fastq.gz",
"s3_uri": "s3://igvf-files/2024/06/01/019c02f8-1822-4efd-a61a-7fd46a28d45a/IGVFFI1752SCWZ.fastq.gz",
"sequencing_platform": "/platform-terms/EFO_0008565/",
"status": "released",
"submitted_file_name": "/oak/stanford/groups/engreitz/Projects/Cohesin/220308B014_CCND1_SSFA2_FAM3C/fastq_trim/FAM3C-Auxin6hrs-FF1-BinF-PCR4-Rep1_S198_R1_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/configuration-files/IGVFFI9937DSFB/",
"accession": "IGVFFI9937DSFB",
"aliases": [
"jesse-engreitz:seqspecfile_CRUDO_FAM3C_Auxin6hrs-FF1-BinF-PCR2-Rep1_S144"
],
"content_type": "seqspec",
"creation_timestamp": "2024-06-11T20:44:07.097511+00:00",
"file_format": "yaml",
"file_size": 915,
"href": "/configuration-files/IGVFFI9937DSFB/@@download/IGVFFI9937DSFB.yaml.gz",
"s3_uri": "s3://igvf-files/2024/06/11/b74160f4-3c6a-472b-91b1-22e773e8ca36/IGVFFI9937DSFB.yaml.gz",
"status": "released",
"submitted_file_name": "/oak/stanford/groups/engreitz/Projects/Cohesin/240410_IGVF_upload/seqspec/guideseq.out.FAM3C_Auxin6hrs-FF1-BinF-PCR2-Rep1_S144.yaml",
"upload_status": "validated"
},
{
"@id": "/configuration-files/IGVFFI4905OMVY/",
"accession": "IGVFFI4905OMVY",
"aliases": [
"jesse-engreitz:seqspecfile_CRUDO_FAM3C_Auxin6hrs-FF1-BinF-PCR4-Rep1_S198"
],
"content_type": "seqspec",
"creation_timestamp": "2024-06-11T20:44:34.348780+00:00",
"file_format": "yaml",
"file_size": 915,
"href": "/configuration-files/IGVFFI4905OMVY/@@download/IGVFFI4905OMVY.yaml.gz",
"s3_uri": "s3://igvf-files/2024/06/11/f96e0a29-b9a3-4db4-83ce-4cfa5f74bcf5/IGVFFI4905OMVY.yaml.gz",
"status": "released",
"submitted_file_name": "/oak/stanford/groups/engreitz/Projects/Cohesin/240410_IGVF_upload/seqspec/guideseq.out.FAM3C_Auxin6hrs-FF1-BinF-PCR4-Rep1_S198.yaml",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI3818YHBA/",
"accession": "IGVFFI3818YHBA",
"aliases": [
"jesse-engreitz:auxiliary_file_CRUDO_FAM3C_Auxin6hrs-FF1-BinF-PCR3-Rep1_S192"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2024-06-01T01:54:11.574431+00:00",
"file_format": "fastq",
"file_size": 40722441,
"href": "/sequence-files/IGVFFI3818YHBA/@@download/IGVFFI3818YHBA.fastq.gz",
"s3_uri": "s3://igvf-files/2024/06/01/8c6a0beb-9d37-43ce-83a5-1db0959216ff/IGVFFI3818YHBA.fastq.gz",
"sequencing_platform": "/platform-terms/EFO_0008565/",
"status": "released",
"submitted_file_name": "/oak/stanford/groups/engreitz/Projects/Cohesin/220308B014_CCND1_SSFA2_FAM3C/fastq_trim/FAM3C-Auxin6hrs-FF1-BinF-PCR3-Rep1_S192_R1_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/configuration-files/IGVFFI9544ZFOX/",
"accession": "IGVFFI9544ZFOX",
"aliases": [
"jesse-engreitz:seqspecfile_CRUDO_FAM3C_Auxin6hrs-FF1-BinF-PCR3-Rep1_S192"
],
"content_type": "seqspec",
"creation_timestamp": "2024-06-11T20:44:20.711049+00:00",
"file_format": "yaml",
"file_size": 915,
"href": "/configuration-files/IGVFFI9544ZFOX/@@download/IGVFFI9544ZFOX.yaml.gz",
"s3_uri": "s3://igvf-files/2024/06/11/94376427-aae2-4c25-84a7-26dc4dbfc78a/IGVFFI9544ZFOX.yaml.gz",
"status": "released",
"submitted_file_name": "/oak/stanford/groups/engreitz/Projects/Cohesin/240410_IGVF_upload/seqspec/guideseq.out.FAM3C_Auxin6hrs-FF1-BinF-PCR3-Rep1_S192.yaml",
"upload_status": "validated"
}
],
"input_for": [
"/analysis-sets/IGVFDS5239VQTN/"
],
"lab": {
"@id": "/labs/jesse-engreitz/",
"title": "Jesse Engreitz, Stanford"
},
"measurement_sets": [
{
"@id": "/measurement-sets/IGVFDS6901XNIT/",
"accession": "IGVFDS6901XNIT",
"aliases": [
"jesse-engreitz:measurement_CRUDO_FAM3C_Auxin6hrs-FF1-BinF-PCR1-Rep1_S138",
"jesse-engreitz:measurement_CRUDO_FAM3C_Auxin6hrs-FF1-BinF-PCR2-Rep1_S144",
"jesse-engreitz:measurement_CRUDO_FAM3C_Auxin6hrs-FF1-BinF-PCR3-Rep1_S192",
"jesse-engreitz:measurement_CRUDO_FAM3C_Auxin6hrs-FF1-BinF-PCR4-Rep1_S198"
],
"preferred_assay_title": "CRISPR FlowFISH screen",
"status": "released"
}
],
"release_timestamp": "2024-07-10T20:12:41.231454+00:00",
"samples": [
{
"@id": "/in-vitro-systems/IGVFSM2608ULOG/",
"@type": [
"InVitroSystem",
"Biosample",
"Sample",
"Item"
],
"accession": "IGVFSM2608ULOG",
"aliases": [
"jesse-engreitz:in-vitro-system_CRUDO_FAM3C_Auxin6hrs-FF1-BinF-PCR1-Rep1_S138",
"jesse-engreitz:in-vitro-system_CRUDO_FAM3C_Auxin6hrs-FF1-BinF-PCR2-Rep1_S144",
"jesse-engreitz:in-vitro-system_CRUDO_FAM3C_Auxin6hrs-FF1-BinF-PCR3-Rep1_S192",
"jesse-engreitz:in-vitro-system_CRUDO_FAM3C_Auxin6hrs-FF1-BinF-PCR4-Rep1_S198"
],
"classifications": [
"cell line"
],
"construct_library_sets": [
"/construct-library-sets/IGVFDS1891GTLU/"
],
"modifications": [
{
"@id": "/degron-modifications/95081d1b-08b4-49ed-b324-e53fc43d8456/",
"modality": "degradation",
"status": "released"
},
{
"@id": "/crispr-modifications/8543fa06-1720-4e7d-8e8f-7e24c1b1cf79/",
"modality": "interference",
"status": "released"
}
],
"sample_terms": [
{
"@id": "/sample-terms/EFO_0002824/",
"@type": [
"SampleTerm",
"OntologyTerm",
"Item"
],
"aliases": [
"igvf:HCT116"
],
"status": "released",
"summary": "HCT116",
"term_name": "HCT116"
}
],
"status": "released",
"summary": "HCT116 cell line, male, Homo sapiens (sorting details: FACS bin F for 80-100% expression of FAM3C) treated with 1 μM 5-Phenyl-1H-indole-3-acetic acid for 6 hours, modified with AID system targeting RAD21, CRISPRi Sp-dCas9-KOX1-KRAB, transfected with a guide library",
"taxa": "Homo sapiens",
"treatments": [
{
"@id": "/treatments/d35868d1-c45b-49ae-8ff3-a9c0c22551c2/",
"status": "released",
"treatment_term_name": "5-Phenyl-1H-indole-3-acetic acid"
}
]
}
],
"schema_version": "12",
"status": "released",
"submitted_by": {
"@id": "/users/3bd6f74c-8cf3-4c35-a94d-0c7c11654815/",
"title": "Chongyon Park"
},
"submitted_files_timestamp": "2024-06-01T01:53:34.859990+00:00",
"summary": "gRNA sequencing for mixed CRISPR FlowFISH screen integrating a guide (sgRNA) library targeting accessible genome regions in many genomic loci",
"uuid": "17b1e54e-59f7-491e-9fda-b8760b8ce467"
}