{
"@context": "/terms/",
"@id": "/auxiliary-sets/IGVFDS1409CHZY/",
"@type": [
"AuxiliarySet",
"FileSet",
"Item"
],
"accession": "IGVFDS1409CHZY",
"aliases": [
"jesse-engreitz:auxiliary_CRUDO_KITLG-Auxin0hrs-FF2-BinB-PCR1_S14",
"jesse-engreitz:auxiliary_CRUDO_KITLG-Auxin0hrs-FF2-BinB-PCR2_S20",
"jesse-engreitz:auxiliary_CRUDO_KITLG-Auxin0hrs-FF2-BinB-PCR3_S110",
"jesse-engreitz:auxiliary_CRUDO_KITLG-Auxin0hrs-FF2-BinB-PCR4_S116"
],
"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 [IGVFDS1409CHZY](/auxiliary-sets/IGVFDS1409CHZY/) has sequence file(s) [IGVFFI6322UNED](/sequence-files/IGVFFI6322UNED/), [IGVFFI2295FIDE](/sequence-files/IGVFFI2295FIDE/), [IGVFFI1480XPQY](/sequence-files/IGVFFI1480XPQY/), [IGVFFI3742XLEW](/sequence-files/IGVFFI3742XLEW/) 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/IGVFDS1409CHZY/"
},
{
"category": "missing analysis",
"detail": "Auxiliary set [IGVFDS1409CHZY](/auxiliary-sets/IGVFDS1409CHZY/) 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/IGVFDS1409CHZY/"
}
]
},
"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": "2024-05-16T17:41:29.543547+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/IGVFFI6322UNED/",
"accession": "IGVFFI6322UNED",
"aliases": [
"jesse-engreitz:auxiliary_file_CRUDO_KITLG-Auxin0hrs-FF2-BinB-PCR1_S14"
],
"content_type": "reads",
"creation_timestamp": "2024-06-01T02:14:32.672890+00:00",
"file_format": "fastq",
"file_size": 12935220,
"href": "/sequence-files/IGVFFI6322UNED/@@download/IGVFFI6322UNED.fastq.gz",
"s3_uri": "s3://igvf-files/2024/06/01/73b62078-85ac-448b-a8ff-282b1517d103/IGVFFI6322UNED.fastq.gz",
"sequencing_platform": "/platform-terms/EFO_0008565/",
"submitted_file_name": "/oak/stanford/groups/engreitz/Projects/Cohesin/220104B013_Cohesin_KITLG/fastq_trim/Auxin0hrs-FF2-BinB-PCR1_S14_R1_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/configuration-files/IGVFFI1101JVSO/",
"accession": "IGVFFI1101JVSO",
"aliases": [
"jesse-engreitz:seqspecfile_CRUDO_KITLG-Auxin0hrs-FF2-BinB-PCR1_S14"
],
"content_type": "seqspec",
"creation_timestamp": "2024-06-11T22:06:37.434450+00:00",
"file_format": "yaml",
"file_size": 901,
"href": "/configuration-files/IGVFFI1101JVSO/@@download/IGVFFI1101JVSO.yaml.gz",
"s3_uri": "s3://igvf-files/2024/06/11/f5241286-e55c-4fd4-8790-dce86654e02c/IGVFFI1101JVSO.yaml.gz",
"submitted_file_name": "/oak/stanford/groups/engreitz/Projects/Cohesin/240410_IGVF_upload/seqspec/guideseq.out.Auxin0hrs-FF2-BinB-PCR1_S14.yaml",
"upload_status": "validated"
},
{
"@id": "/configuration-files/IGVFFI0936XUFD/",
"accession": "IGVFFI0936XUFD",
"aliases": [
"jesse-engreitz:seqspecfile_CRUDO_KITLG-Auxin0hrs-FF2-BinB-PCR2_S20"
],
"content_type": "seqspec",
"creation_timestamp": "2024-06-11T22:06:50.750952+00:00",
"file_format": "yaml",
"file_size": 903,
"href": "/configuration-files/IGVFFI0936XUFD/@@download/IGVFFI0936XUFD.yaml.gz",
"s3_uri": "s3://igvf-files/2024/06/11/9f7b92a2-ed0d-4605-9d61-041756886ea1/IGVFFI0936XUFD.yaml.gz",
"submitted_file_name": "/oak/stanford/groups/engreitz/Projects/Cohesin/240410_IGVF_upload/seqspec/guideseq.out.Auxin0hrs-FF2-BinB-PCR2_S20.yaml",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI2295FIDE/",
"accession": "IGVFFI2295FIDE",
"aliases": [
"jesse-engreitz:auxiliary_file_CRUDO_KITLG-Auxin0hrs-FF2-BinB-PCR3_S110"
],
"content_type": "reads",
"creation_timestamp": "2024-06-01T02:16:51.905012+00:00",
"file_format": "fastq",
"file_size": 26958877,
"href": "/sequence-files/IGVFFI2295FIDE/@@download/IGVFFI2295FIDE.fastq.gz",
"s3_uri": "s3://igvf-files/2024/06/01/ed044620-4602-4b9b-8ac6-ccdbe609cf2b/IGVFFI2295FIDE.fastq.gz",
"sequencing_platform": "/platform-terms/EFO_0008565/",
"submitted_file_name": "/oak/stanford/groups/engreitz/Projects/Cohesin/220104B013_Cohesin_KITLG/fastq_trim/Auxin0hrs-FF2-BinB-PCR3_S110_R1_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI1480XPQY/",
"accession": "IGVFFI1480XPQY",
"aliases": [
"jesse-engreitz:auxiliary_file_CRUDO_KITLG-Auxin0hrs-FF2-BinB-PCR4_S116"
],
"content_type": "reads",
"creation_timestamp": "2024-06-01T02:17:10.409332+00:00",
"file_format": "fastq",
"file_size": 21673848,
"href": "/sequence-files/IGVFFI1480XPQY/@@download/IGVFFI1480XPQY.fastq.gz",
"s3_uri": "s3://igvf-files/2024/06/01/13434af9-a1a5-46eb-a7e5-17429408565a/IGVFFI1480XPQY.fastq.gz",
"sequencing_platform": "/platform-terms/EFO_0008565/",
"submitted_file_name": "/oak/stanford/groups/engreitz/Projects/Cohesin/220104B013_Cohesin_KITLG/fastq_trim/Auxin0hrs-FF2-BinB-PCR4_S116_R1_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI3742XLEW/",
"accession": "IGVFFI3742XLEW",
"aliases": [
"jesse-engreitz:auxiliary_file_CRUDO_KITLG-Auxin0hrs-FF2-BinB-PCR2_S20"
],
"content_type": "reads",
"creation_timestamp": "2024-06-01T02:14:50.249863+00:00",
"file_format": "fastq",
"file_size": 10426667,
"href": "/sequence-files/IGVFFI3742XLEW/@@download/IGVFFI3742XLEW.fastq.gz",
"s3_uri": "s3://igvf-files/2024/06/01/e48f4af8-1217-4d52-bd48-915fd4433eb9/IGVFFI3742XLEW.fastq.gz",
"sequencing_platform": "/platform-terms/EFO_0008565/",
"submitted_file_name": "/oak/stanford/groups/engreitz/Projects/Cohesin/220104B013_Cohesin_KITLG/fastq_trim/Auxin0hrs-FF2-BinB-PCR2_S20_R1_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/configuration-files/IGVFFI8160QJHC/",
"accession": "IGVFFI8160QJHC",
"aliases": [
"jesse-engreitz:seqspecfile_CRUDO_KITLG-Auxin0hrs-FF2-BinB-PCR4_S116"
],
"content_type": "seqspec",
"creation_timestamp": "2024-06-11T22:07:17.713725+00:00",
"file_format": "yaml",
"file_size": 904,
"href": "/configuration-files/IGVFFI8160QJHC/@@download/IGVFFI8160QJHC.yaml.gz",
"s3_uri": "s3://igvf-files/2024/06/11/e2efbf39-2690-420a-b234-62621076d690/IGVFFI8160QJHC.yaml.gz",
"submitted_file_name": "/oak/stanford/groups/engreitz/Projects/Cohesin/240410_IGVF_upload/seqspec/guideseq.out.Auxin0hrs-FF2-BinB-PCR4_S116.yaml",
"upload_status": "validated"
},
{
"@id": "/configuration-files/IGVFFI0141MIOQ/",
"accession": "IGVFFI0141MIOQ",
"aliases": [
"jesse-engreitz:seqspecfile_CRUDO_KITLG-Auxin0hrs-FF2-BinB-PCR3_S110"
],
"content_type": "seqspec",
"creation_timestamp": "2024-06-11T22:07:04.569484+00:00",
"file_format": "yaml",
"file_size": 902,
"href": "/configuration-files/IGVFFI0141MIOQ/@@download/IGVFFI0141MIOQ.yaml.gz",
"s3_uri": "s3://igvf-files/2024/06/11/cd1bf0b3-5adc-4641-92d0-f436efbd28f3/IGVFFI0141MIOQ.yaml.gz",
"submitted_file_name": "/oak/stanford/groups/engreitz/Projects/Cohesin/240410_IGVF_upload/seqspec/guideseq.out.Auxin0hrs-FF2-BinB-PCR3_S110.yaml",
"upload_status": "validated"
}
],
"input_file_set_for": [],
"lab": {
"@id": "/labs/jesse-engreitz/",
"title": "Jesse Engreitz, Stanford"
},
"measurement_sets": [
{
"@id": "/measurement-sets/IGVFDS7147ANAC/",
"accession": "IGVFDS7147ANAC",
"aliases": [
"jesse-engreitz:measurement_CRUDO_KITLG-Auxin0hrs-FF2-BinB-PCR1_S14",
"jesse-engreitz:measurement_CRUDO_KITLG-Auxin0hrs-FF2-BinB-PCR2_S20",
"jesse-engreitz:measurement_CRUDO_KITLG-Auxin0hrs-FF2-BinB-PCR3_S110",
"jesse-engreitz:measurement_CRUDO_KITLG-Auxin0hrs-FF2-BinB-PCR4_S116"
],
"preferred_assay_title": "CRISPR FlowFISH screen"
}
],
"release_timestamp": "2024-07-10T20:14:19.913601+00:00",
"samples": [
{
"@id": "/in-vitro-systems/IGVFSM3263KXLP/",
"@type": [
"InVitroSystem",
"Biosample",
"Sample",
"Item"
],
"accession": "IGVFSM3263KXLP",
"aliases": [
"jesse-engreitz:in-vitro-system_CRUDO_KITLG-Auxin0hrs-FF2-BinB-PCR1_S14",
"jesse-engreitz:in-vitro-system_CRUDO_KITLG-Auxin0hrs-FF2-BinB-PCR2_S20",
"jesse-engreitz:in-vitro-system_CRUDO_KITLG-Auxin0hrs-FF2-BinB-PCR3_S110",
"jesse-engreitz:in-vitro-system_CRUDO_KITLG-Auxin0hrs-FF2-BinB-PCR4_S116"
],
"classifications": [
"cell line"
],
"construct_library_sets": [
"/construct-library-sets/IGVFDS7846UISG/"
],
"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 B for 10-20% expression of KITLG) 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": "2024-06-01T02:14:32.672890+00:00",
"summary": "gRNA sequencing for CRISPR interference FlowFISH screen integrating a guide (sgRNA) library targeting accessible genome regions in many genomic loci",
"uuid": "1a47afd9-57f5-4ea0-90b9-ff6f89d85f66"
}