{
"@context": "/terms/",
"@id": "/auxiliary-sets/IGVFDS9816UKEE/",
"@type": [
"AuxiliarySet",
"FileSet",
"Item"
],
"accession": "IGVFDS9816UKEE",
"aliases": [
"jesse-engreitz:auxiliary_CRUDO_CCND1_Auxin0hrs-FF1-BinC-PCR1-Rep1_S219",
"jesse-engreitz:auxiliary_CRUDO_CCND1_Auxin0hrs-FF1-BinC-PCR2-Rep1_S225",
"jesse-engreitz:auxiliary_CRUDO_CCND1_Auxin0hrs-FF1-BinC-PCR3-Rep1_S261",
"jesse-engreitz:auxiliary_CRUDO_CCND1_Auxin0hrs-FF1-BinC-PCR4-Rep1_S267"
],
"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 [IGVFDS9816UKEE](/auxiliary-sets/IGVFDS9816UKEE/) has sequence file(s) [IGVFFI0281SSVE](/sequence-files/IGVFFI0281SSVE/), [IGVFFI4666APET](/sequence-files/IGVFFI4666APET/), [IGVFFI6628DNUA](/sequence-files/IGVFFI6628DNUA/), [IGVFFI6676HNDS](/sequence-files/IGVFFI6676HNDS/) 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/IGVFDS9816UKEE/"
},
{
"category": "missing analysis",
"detail": "Auxiliary set [IGVFDS9816UKEE](/auxiliary-sets/IGVFDS9816UKEE/) 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/IGVFDS9816UKEE/"
}
]
},
"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": "2024-05-13T22:38:47.107623+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/IGVFFI0281SSVE/",
"accession": "IGVFFI0281SSVE",
"aliases": [
"jesse-engreitz:auxiliary_file_CRUDO_CCND1_Auxin0hrs-FF1-BinC-PCR1-Rep1_S219"
],
"content_type": "reads",
"creation_timestamp": "2024-06-01T01:36:02.300105+00:00",
"file_format": "fastq",
"file_size": 23741843,
"href": "/sequence-files/IGVFFI0281SSVE/@@download/IGVFFI0281SSVE.fastq.gz",
"s3_uri": "s3://igvf-files/2024/06/01/6b4ccd84-7aa2-4b21-b997-a6e772389b8d/IGVFFI0281SSVE.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-FF1-BinC-PCR1-Rep1_S219_R1_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/configuration-files/IGVFFI2850JSOK/",
"accession": "IGVFFI2850JSOK",
"aliases": [
"jesse-engreitz:seqspecfile_CRUDO_CCND1_Auxin0hrs-FF1-BinC-PCR1-Rep1_S219"
],
"content_type": "seqspec",
"creation_timestamp": "2024-06-11T20:28:03.099293+00:00",
"file_format": "yaml",
"file_size": 913,
"href": "/configuration-files/IGVFFI2850JSOK/@@download/IGVFFI2850JSOK.yaml.gz",
"s3_uri": "s3://igvf-files/2024/06/11/11202222-20d2-4ca4-a398-a6f5cf5b6f06/IGVFFI2850JSOK.yaml.gz",
"submitted_file_name": "/oak/stanford/groups/engreitz/Projects/Cohesin/240410_IGVF_upload/seqspec/guideseq.out.CCND1_Auxin0hrs-FF1-BinC-PCR1-Rep1_S219.yaml",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI4666APET/",
"accession": "IGVFFI4666APET",
"aliases": [
"jesse-engreitz:auxiliary_file_CRUDO_CCND1_Auxin0hrs-FF1-BinC-PCR2-Rep1_S225"
],
"content_type": "reads",
"creation_timestamp": "2024-06-01T01:36:20.061604+00:00",
"file_format": "fastq",
"file_size": 19586330,
"href": "/sequence-files/IGVFFI4666APET/@@download/IGVFFI4666APET.fastq.gz",
"s3_uri": "s3://igvf-files/2024/06/01/3655fc84-0222-4c07-89bb-87b14abae1cc/IGVFFI4666APET.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-FF1-BinC-PCR2-Rep1_S225_R1_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI6628DNUA/",
"accession": "IGVFFI6628DNUA",
"aliases": [
"jesse-engreitz:auxiliary_file_CRUDO_CCND1_Auxin0hrs-FF1-BinC-PCR3-Rep1_S261"
],
"content_type": "reads",
"creation_timestamp": "2024-06-01T01:36:38.439911+00:00",
"file_format": "fastq",
"file_size": 23792398,
"href": "/sequence-files/IGVFFI6628DNUA/@@download/IGVFFI6628DNUA.fastq.gz",
"s3_uri": "s3://igvf-files/2024/06/01/1fe08c33-546f-47cc-95e7-aef43a5ea15c/IGVFFI6628DNUA.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-FF1-BinC-PCR3-Rep1_S261_R1_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI6676HNDS/",
"accession": "IGVFFI6676HNDS",
"aliases": [
"jesse-engreitz:auxiliary_file_CRUDO_CCND1_Auxin0hrs-FF1-BinC-PCR4-Rep1_S267"
],
"content_type": "reads",
"creation_timestamp": "2024-06-01T01:36:56.673095+00:00",
"file_format": "fastq",
"file_size": 27428664,
"href": "/sequence-files/IGVFFI6676HNDS/@@download/IGVFFI6676HNDS.fastq.gz",
"s3_uri": "s3://igvf-files/2024/06/01/fbe1f7cc-4ab5-44c6-9e89-784e9759a86b/IGVFFI6676HNDS.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-FF1-BinC-PCR4-Rep1_S267_R1_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/configuration-files/IGVFFI9157ATYV/",
"accession": "IGVFFI9157ATYV",
"aliases": [
"jesse-engreitz:seqspecfile_CRUDO_CCND1_Auxin0hrs-FF1-BinC-PCR3-Rep1_S261"
],
"content_type": "seqspec",
"creation_timestamp": "2024-06-11T20:28:31.944623+00:00",
"file_format": "yaml",
"file_size": 913,
"href": "/configuration-files/IGVFFI9157ATYV/@@download/IGVFFI9157ATYV.yaml.gz",
"s3_uri": "s3://igvf-files/2024/06/11/1a92a8ae-ac33-4857-b008-db0a40dd35f1/IGVFFI9157ATYV.yaml.gz",
"submitted_file_name": "/oak/stanford/groups/engreitz/Projects/Cohesin/240410_IGVF_upload/seqspec/guideseq.out.CCND1_Auxin0hrs-FF1-BinC-PCR3-Rep1_S261.yaml",
"upload_status": "validated"
},
{
"@id": "/configuration-files/IGVFFI0373UCGE/",
"accession": "IGVFFI0373UCGE",
"aliases": [
"jesse-engreitz:seqspecfile_CRUDO_CCND1_Auxin0hrs-FF1-BinC-PCR4-Rep1_S267"
],
"content_type": "seqspec",
"creation_timestamp": "2024-06-11T20:28:46.307088+00:00",
"file_format": "yaml",
"file_size": 913,
"href": "/configuration-files/IGVFFI0373UCGE/@@download/IGVFFI0373UCGE.yaml.gz",
"s3_uri": "s3://igvf-files/2024/06/11/b99d0146-9044-4397-9818-4884b859d38d/IGVFFI0373UCGE.yaml.gz",
"submitted_file_name": "/oak/stanford/groups/engreitz/Projects/Cohesin/240410_IGVF_upload/seqspec/guideseq.out.CCND1_Auxin0hrs-FF1-BinC-PCR4-Rep1_S267.yaml",
"upload_status": "validated"
},
{
"@id": "/configuration-files/IGVFFI9386BVXR/",
"accession": "IGVFFI9386BVXR",
"aliases": [
"jesse-engreitz:seqspecfile_CRUDO_CCND1_Auxin0hrs-FF1-BinC-PCR2-Rep1_S225"
],
"content_type": "seqspec",
"creation_timestamp": "2024-06-11T20:28:18.053492+00:00",
"file_format": "yaml",
"file_size": 912,
"href": "/configuration-files/IGVFFI9386BVXR/@@download/IGVFFI9386BVXR.yaml.gz",
"s3_uri": "s3://igvf-files/2024/06/11/e0d94c4c-66cb-457b-b5dd-c4f7fee7c665/IGVFFI9386BVXR.yaml.gz",
"submitted_file_name": "/oak/stanford/groups/engreitz/Projects/Cohesin/240410_IGVF_upload/seqspec/guideseq.out.CCND1_Auxin0hrs-FF1-BinC-PCR2-Rep1_S225.yaml",
"upload_status": "validated"
}
],
"input_file_set_for": [],
"lab": {
"@id": "/labs/jesse-engreitz/",
"title": "Jesse Engreitz, Stanford"
},
"measurement_sets": [
{
"@id": "/measurement-sets/IGVFDS0528ZIOC/",
"accession": "IGVFDS0528ZIOC",
"aliases": [
"jesse-engreitz:measurement_CRUDO_CCND1_Auxin0hrs-FF1-BinC-PCR1-Rep1_S219",
"jesse-engreitz:measurement_CRUDO_CCND1_Auxin0hrs-FF1-BinC-PCR2-Rep1_S225",
"jesse-engreitz:measurement_CRUDO_CCND1_Auxin0hrs-FF1-BinC-PCR3-Rep1_S261",
"jesse-engreitz:measurement_CRUDO_CCND1_Auxin0hrs-FF1-BinC-PCR4-Rep1_S267"
],
"preferred_assay_title": "CRISPR FlowFISH screen"
}
],
"release_timestamp": "2024-07-10T20:08:04.007903+00:00",
"samples": [
{
"@id": "/in-vitro-systems/IGVFSM2913DQHN/",
"@type": [
"InVitroSystem",
"Biosample",
"Sample",
"Item"
],
"accession": "IGVFSM2913DQHN",
"aliases": [
"jesse-engreitz:in-vitro-system_CRUDO_CCND1_Auxin0hrs-FF1-BinC-PCR1-Rep1_S219",
"jesse-engreitz:in-vitro-system_CRUDO_CCND1_Auxin0hrs-FF1-BinC-PCR2-Rep1_S225",
"jesse-engreitz:in-vitro-system_CRUDO_CCND1_Auxin0hrs-FF1-BinC-PCR3-Rep1_S261",
"jesse-engreitz:in-vitro-system_CRUDO_CCND1_Auxin0hrs-FF1-BinC-PCR4-Rep1_S267"
],
"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 C for 35-45% 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": "2024-06-01T01:36:02.300105+00:00",
"summary": "gRNA sequencing for CRISPR interference FlowFISH screen integrating a guide (sgRNA) library targeting accessible genome regions in many genomic loci",
"uuid": "f3949b3c-2664-470c-ad45-3ee06d534a0c"
}