{
"@context": "/terms/",
"@id": "/auxiliary-sets/IGVFDS2403ZERE/",
"@type": [
"AuxiliarySet",
"FileSet",
"Item"
],
"accession": "IGVFDS2403ZERE",
"aliases": [
"jesse-engreitz:auxiliary_CRUDO_CCND1_Auxin0hrs-FF2-BinD-PCR1-Rep1_S232",
"jesse-engreitz:auxiliary_CRUDO_CCND1_Auxin0hrs-FF2-BinD-PCR2-Rep1_S238",
"jesse-engreitz:auxiliary_CRUDO_CCND1_Auxin0hrs-FF2-BinD-PCR3-Rep1_S274",
"jesse-engreitz:auxiliary_CRUDO_CCND1_Auxin0hrs-FF2-BinD-PCR4-Rep1_S280"
],
"audit": {
"INTERNAL_ACTION": [
{
"category": "mismatched status",
"detail": "Released human donor [IGVFDO0384OZRW](/human-donors/IGVFDO0384OZRW/) has in progress subobject publication [155f24ce-5c2c-4400-8651-da9447eaca25](/publications/155f24ce-5c2c-4400-8651-da9447eaca25/).",
"level": 30,
"level_name": "INTERNAL_ACTION",
"name": "audit_item_status",
"path": "/human-donors/IGVFDO0384OZRW/"
}
],
"WARNING": [
{
"category": "missing sequencing kit",
"detail": "Auxiliary set [IGVFDS2403ZERE](/auxiliary-sets/IGVFDS2403ZERE/) has sequence file(s) [IGVFFI9017LLWY](/sequence-files/IGVFFI9017LLWY/), [IGVFFI7774KVKB](/sequence-files/IGVFFI7774KVKB/), [IGVFFI6030SAOG](/sequence-files/IGVFFI6030SAOG/), [IGVFFI8172OMRE](/sequence-files/IGVFFI8172OMRE/) 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/IGVFDS2403ZERE/"
},
{
"category": "missing analysis",
"detail": "Auxiliary set [IGVFDS2403ZERE](/auxiliary-sets/IGVFDS2403ZERE/) is a raw data set with files, but is not listed in any `input_file_sets` for any analysis sets. Raw data sets with files are expected to be associated with at least one analysis set.",
"level": 40,
"level_name": "WARNING",
"name": "audit_input_file_set_for",
"path": "/auxiliary-sets/IGVFDS2403ZERE/"
}
]
},
"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": "2024-05-13T22:39:15.099118+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/IGVFFI9017LLWY/",
"accession": "IGVFFI9017LLWY",
"aliases": [
"jesse-engreitz:auxiliary_file_CRUDO_CCND1_Auxin0hrs-FF2-BinD-PCR1-Rep1_S232"
],
"content_type": "reads",
"creation_timestamp": "2024-06-01T01:37:17.550617+00:00",
"file_format": "fastq",
"file_size": 19145096,
"href": "/sequence-files/IGVFFI9017LLWY/@@download/IGVFFI9017LLWY.fastq.gz",
"s3_uri": "s3://igvf-files/2024/06/01/f76e5b80-83be-451f-af1c-c2e12a4ea06c/IGVFFI9017LLWY.fastq.gz",
"sequencing_platform": "/platform-terms/EFO_0008565/",
"submitted_file_name": "/oak/stanford/groups/engreitz/Projects/Cohesin/220308B014_CCND1_SSFA2_FAM3C/fastq_trim/CCND1-Auxin0hrs-FF2-BinD-PCR1-Rep1_S232_R1_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/configuration-files/IGVFFI3301LAMU/",
"accession": "IGVFFI3301LAMU",
"aliases": [
"jesse-engreitz:seqspecfile_CRUDO_CCND1_Auxin0hrs-FF2-BinD-PCR1-Rep1_S232"
],
"content_type": "seqspec",
"creation_timestamp": "2024-06-11T20:29:03.395319+00:00",
"file_format": "yaml",
"file_size": 915,
"href": "/configuration-files/IGVFFI3301LAMU/@@download/IGVFFI3301LAMU.yaml.gz",
"s3_uri": "s3://igvf-files/2024/06/11/e136e748-bcda-41c1-946b-f1991edb189a/IGVFFI3301LAMU.yaml.gz",
"submitted_file_name": "/oak/stanford/groups/engreitz/Projects/Cohesin/240410_IGVF_upload/seqspec/guideseq.out.CCND1_Auxin0hrs-FF2-BinD-PCR1-Rep1_S232.yaml",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI7774KVKB/",
"accession": "IGVFFI7774KVKB",
"aliases": [
"jesse-engreitz:auxiliary_file_CRUDO_CCND1_Auxin0hrs-FF2-BinD-PCR2-Rep1_S238"
],
"content_type": "reads",
"creation_timestamp": "2024-06-01T01:37:35.348521+00:00",
"file_format": "fastq",
"file_size": 18935065,
"href": "/sequence-files/IGVFFI7774KVKB/@@download/IGVFFI7774KVKB.fastq.gz",
"s3_uri": "s3://igvf-files/2024/06/01/c96f8bd5-5c9f-4e8f-bbfc-5e9b913555f5/IGVFFI7774KVKB.fastq.gz",
"sequencing_platform": "/platform-terms/EFO_0008565/",
"submitted_file_name": "/oak/stanford/groups/engreitz/Projects/Cohesin/220308B014_CCND1_SSFA2_FAM3C/fastq_trim/CCND1-Auxin0hrs-FF2-BinD-PCR2-Rep1_S238_R1_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI6030SAOG/",
"accession": "IGVFFI6030SAOG",
"aliases": [
"jesse-engreitz:auxiliary_file_CRUDO_CCND1_Auxin0hrs-FF2-BinD-PCR3-Rep1_S274"
],
"content_type": "reads",
"creation_timestamp": "2024-06-01T01:37:53.123405+00:00",
"file_format": "fastq",
"file_size": 24245776,
"href": "/sequence-files/IGVFFI6030SAOG/@@download/IGVFFI6030SAOG.fastq.gz",
"s3_uri": "s3://igvf-files/2024/06/01/93a6bfd4-f546-4268-9d4c-36e2eb5dedc5/IGVFFI6030SAOG.fastq.gz",
"sequencing_platform": "/platform-terms/EFO_0008565/",
"submitted_file_name": "/oak/stanford/groups/engreitz/Projects/Cohesin/220308B014_CCND1_SSFA2_FAM3C/fastq_trim/CCND1-Auxin0hrs-FF2-BinD-PCR3-Rep1_S274_R1_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI8172OMRE/",
"accession": "IGVFFI8172OMRE",
"aliases": [
"jesse-engreitz:auxiliary_file_CRUDO_CCND1_Auxin0hrs-FF2-BinD-PCR4-Rep1_S280"
],
"content_type": "reads",
"creation_timestamp": "2024-06-01T01:38:15.440089+00:00",
"file_format": "fastq",
"file_size": 24490365,
"href": "/sequence-files/IGVFFI8172OMRE/@@download/IGVFFI8172OMRE.fastq.gz",
"s3_uri": "s3://igvf-files/2024/06/01/5df06ec8-2c66-4755-82ca-33d90a801d29/IGVFFI8172OMRE.fastq.gz",
"sequencing_platform": "/platform-terms/EFO_0008565/",
"submitted_file_name": "/oak/stanford/groups/engreitz/Projects/Cohesin/220308B014_CCND1_SSFA2_FAM3C/fastq_trim/CCND1-Auxin0hrs-FF2-BinD-PCR4-Rep1_S280_R1_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/configuration-files/IGVFFI9558UYBL/",
"accession": "IGVFFI9558UYBL",
"aliases": [
"jesse-engreitz:seqspecfile_CRUDO_CCND1_Auxin0hrs-FF2-BinD-PCR3-Rep1_S274"
],
"content_type": "seqspec",
"creation_timestamp": "2024-06-11T20:29:31.272162+00:00",
"file_format": "yaml",
"file_size": 912,
"href": "/configuration-files/IGVFFI9558UYBL/@@download/IGVFFI9558UYBL.yaml.gz",
"s3_uri": "s3://igvf-files/2024/06/11/987616fe-7d14-4324-9ad0-77ae7de1bd76/IGVFFI9558UYBL.yaml.gz",
"submitted_file_name": "/oak/stanford/groups/engreitz/Projects/Cohesin/240410_IGVF_upload/seqspec/guideseq.out.CCND1_Auxin0hrs-FF2-BinD-PCR3-Rep1_S274.yaml",
"upload_status": "validated"
},
{
"@id": "/configuration-files/IGVFFI7568TJSW/",
"accession": "IGVFFI7568TJSW",
"aliases": [
"jesse-engreitz:seqspecfile_CRUDO_CCND1_Auxin0hrs-FF2-BinD-PCR4-Rep1_S280"
],
"content_type": "seqspec",
"creation_timestamp": "2024-06-11T20:29:45.264881+00:00",
"file_format": "yaml",
"file_size": 914,
"href": "/configuration-files/IGVFFI7568TJSW/@@download/IGVFFI7568TJSW.yaml.gz",
"s3_uri": "s3://igvf-files/2024/06/11/248276f3-e5c5-42db-b72d-10163dd224b6/IGVFFI7568TJSW.yaml.gz",
"submitted_file_name": "/oak/stanford/groups/engreitz/Projects/Cohesin/240410_IGVF_upload/seqspec/guideseq.out.CCND1_Auxin0hrs-FF2-BinD-PCR4-Rep1_S280.yaml",
"upload_status": "validated"
},
{
"@id": "/configuration-files/IGVFFI7108WMVT/",
"accession": "IGVFFI7108WMVT",
"aliases": [
"jesse-engreitz:seqspecfile_CRUDO_CCND1_Auxin0hrs-FF2-BinD-PCR2-Rep1_S238"
],
"content_type": "seqspec",
"creation_timestamp": "2024-06-11T20:29:17.307762+00:00",
"file_format": "yaml",
"file_size": 914,
"href": "/configuration-files/IGVFFI7108WMVT/@@download/IGVFFI7108WMVT.yaml.gz",
"s3_uri": "s3://igvf-files/2024/06/11/021d990e-97f0-4ac5-902c-a9c4e080ec75/IGVFFI7108WMVT.yaml.gz",
"submitted_file_name": "/oak/stanford/groups/engreitz/Projects/Cohesin/240410_IGVF_upload/seqspec/guideseq.out.CCND1_Auxin0hrs-FF2-BinD-PCR2-Rep1_S238.yaml",
"upload_status": "validated"
}
],
"input_file_set_for": [],
"lab": {
"@id": "/labs/jesse-engreitz/",
"title": "Jesse Engreitz, Stanford"
},
"measurement_sets": [
{
"@id": "/measurement-sets/IGVFDS2949NCKP/",
"accession": "IGVFDS2949NCKP",
"aliases": [
"jesse-engreitz:measurement_CRUDO_CCND1_Auxin0hrs-FF2-BinD-PCR1-Rep1_S232",
"jesse-engreitz:measurement_CRUDO_CCND1_Auxin0hrs-FF2-BinD-PCR2-Rep1_S238",
"jesse-engreitz:measurement_CRUDO_CCND1_Auxin0hrs-FF2-BinD-PCR3-Rep1_S274",
"jesse-engreitz:measurement_CRUDO_CCND1_Auxin0hrs-FF2-BinD-PCR4-Rep1_S280"
],
"preferred_assay_title": "CRISPR FlowFISH screen"
}
],
"release_timestamp": "2024-07-10T20:08:50.119317+00:00",
"samples": [
{
"@id": "/in-vitro-systems/IGVFSM9888RFRZ/",
"@type": [
"InVitroSystem",
"Biosample",
"Sample",
"Item"
],
"accession": "IGVFSM9888RFRZ",
"aliases": [
"jesse-engreitz:in-vitro-system_CRUDO_CCND1_Auxin0hrs-FF2-BinD-PCR1-Rep1_S232",
"jesse-engreitz:in-vitro-system_CRUDO_CCND1_Auxin0hrs-FF2-BinD-PCR2-Rep1_S238",
"jesse-engreitz:in-vitro-system_CRUDO_CCND1_Auxin0hrs-FF2-BinD-PCR3-Rep1_S274",
"jesse-engreitz:in-vitro-system_CRUDO_CCND1_Auxin0hrs-FF2-BinD-PCR4-Rep1_S280"
],
"classifications": [
"cell line"
],
"construct_library_sets": [
"/construct-library-sets/IGVFDS6351FGNG/"
],
"modifications": [
"/crispr-modifications/8543fa06-1720-4e7d-8e8f-7e24c1b1cf79/"
],
"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 D for 55-65% expression of CCND1) modified with a guide library",
"taxa": "Homo sapiens"
}
],
"schema_version": "11",
"status": "released",
"submitted_by": {
"@id": "/users/3bd6f74c-8cf3-4c35-a94d-0c7c11654815/",
"title": "Chongyon Park"
},
"submitted_files_timestamp": "2024-06-01T01:37:17.550617+00:00",
"summary": "gRNA sequencing for CRISPR interference FlowFISH screen integrating a guide (sgRNA) library targeting accessible genome regions in many genomic loci",
"uuid": "6c54ecd8-a998-4b9b-b254-2623110a63c9"
}