{
"@context": "/terms/",
"@id": "/auxiliary-sets/IGVFDS6689ALTU/",
"@type": [
"AuxiliarySet",
"FileSet",
"Item"
],
"accession": "IGVFDS6689ALTU",
"aliases": [
"jesse-engreitz:auxiliary_CRUDO_KITLG-Auxin0hrs-FF3-BinA-PCR1_S25",
"jesse-engreitz:auxiliary_CRUDO_KITLG-Auxin0hrs-FF3-BinA-PCR2_S31",
"jesse-engreitz:auxiliary_CRUDO_KITLG-Auxin0hrs-FF3-BinA-PCR3_S121",
"jesse-engreitz:auxiliary_CRUDO_KITLG-Auxin0hrs-FF3-BinA-PCR4_S127"
],
"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 [IGVFDS6689ALTU](/auxiliary-sets/IGVFDS6689ALTU/) has sequence file(s) [IGVFFI1867FHJJ](/sequence-files/IGVFFI1867FHJJ/), [IGVFFI7934CVHY](/sequence-files/IGVFFI7934CVHY/), [IGVFFI0432CSXV](/sequence-files/IGVFFI0432CSXV/), [IGVFFI1136TXZO](/sequence-files/IGVFFI1136TXZO/) 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/IGVFDS6689ALTU/"
},
{
"category": "missing analysis",
"detail": "Auxiliary set [IGVFDS6689ALTU](/auxiliary-sets/IGVFDS6689ALTU/) 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/IGVFDS6689ALTU/"
}
]
},
"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": "2024-05-16T17:41:55.693759+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/IGVFFI1867FHJJ/",
"accession": "IGVFFI1867FHJJ",
"aliases": [
"jesse-engreitz:auxiliary_file_CRUDO_KITLG-Auxin0hrs-FF3-BinA-PCR1_S25"
],
"content_type": "reads",
"creation_timestamp": "2024-06-01T02:17:25.198121+00:00",
"file_format": "fastq",
"file_size": 10296423,
"href": "/sequence-files/IGVFFI1867FHJJ/@@download/IGVFFI1867FHJJ.fastq.gz",
"s3_uri": "s3://igvf-files/2024/06/01/0491b704-c386-41fd-b314-4605e72536b5/IGVFFI1867FHJJ.fastq.gz",
"sequencing_platform": "/platform-terms/EFO_0008565/",
"submitted_file_name": "/oak/stanford/groups/engreitz/Projects/Cohesin/220104B013_Cohesin_KITLG/fastq_trim/Auxin0hrs-FF3-BinA-PCR1_S25_R1_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/configuration-files/IGVFFI0885JBQU/",
"accession": "IGVFFI0885JBQU",
"aliases": [
"jesse-engreitz:seqspecfile_CRUDO_KITLG-Auxin0hrs-FF3-BinA-PCR1_S25"
],
"content_type": "seqspec",
"creation_timestamp": "2024-06-11T22:07:28.945778+00:00",
"file_format": "yaml",
"file_size": 901,
"href": "/configuration-files/IGVFFI0885JBQU/@@download/IGVFFI0885JBQU.yaml.gz",
"s3_uri": "s3://igvf-files/2024/06/11/91d025de-8ffc-404a-af14-a3b61b2546f0/IGVFFI0885JBQU.yaml.gz",
"submitted_file_name": "/oak/stanford/groups/engreitz/Projects/Cohesin/240410_IGVF_upload/seqspec/guideseq.out.Auxin0hrs-FF3-BinA-PCR1_S25.yaml",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI7934CVHY/",
"accession": "IGVFFI7934CVHY",
"aliases": [
"jesse-engreitz:auxiliary_file_CRUDO_KITLG-Auxin0hrs-FF3-BinA-PCR4_S127"
],
"content_type": "reads",
"creation_timestamp": "2024-06-01T02:18:18.725415+00:00",
"file_format": "fastq",
"file_size": 35257742,
"href": "/sequence-files/IGVFFI7934CVHY/@@download/IGVFFI7934CVHY.fastq.gz",
"s3_uri": "s3://igvf-files/2024/06/01/3b524c9f-0679-416b-af85-7c5b4286dd01/IGVFFI7934CVHY.fastq.gz",
"sequencing_platform": "/platform-terms/EFO_0008565/",
"submitted_file_name": "/oak/stanford/groups/engreitz/Projects/Cohesin/220104B013_Cohesin_KITLG/fastq_trim/Auxin0hrs-FF3-BinA-PCR4_S127_R1_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/configuration-files/IGVFFI9488XMEZ/",
"accession": "IGVFFI9488XMEZ",
"aliases": [
"jesse-engreitz:seqspecfile_CRUDO_KITLG-Auxin0hrs-FF3-BinA-PCR2_S31"
],
"content_type": "seqspec",
"creation_timestamp": "2024-06-11T22:07:42.606474+00:00",
"file_format": "yaml",
"file_size": 902,
"href": "/configuration-files/IGVFFI9488XMEZ/@@download/IGVFFI9488XMEZ.yaml.gz",
"s3_uri": "s3://igvf-files/2024/06/11/0397f990-fb19-4459-bfa6-30d6674f23df/IGVFFI9488XMEZ.yaml.gz",
"submitted_file_name": "/oak/stanford/groups/engreitz/Projects/Cohesin/240410_IGVF_upload/seqspec/guideseq.out.Auxin0hrs-FF3-BinA-PCR2_S31.yaml",
"upload_status": "validated"
},
{
"@id": "/configuration-files/IGVFFI1834ADNY/",
"accession": "IGVFFI1834ADNY",
"aliases": [
"jesse-engreitz:seqspecfile_CRUDO_KITLG-Auxin0hrs-FF3-BinA-PCR3_S121"
],
"content_type": "seqspec",
"creation_timestamp": "2024-06-11T22:07:55.694559+00:00",
"file_format": "yaml",
"file_size": 904,
"href": "/configuration-files/IGVFFI1834ADNY/@@download/IGVFFI1834ADNY.yaml.gz",
"s3_uri": "s3://igvf-files/2024/06/11/2a75b4a0-a067-4312-b132-35b30a001402/IGVFFI1834ADNY.yaml.gz",
"submitted_file_name": "/oak/stanford/groups/engreitz/Projects/Cohesin/240410_IGVF_upload/seqspec/guideseq.out.Auxin0hrs-FF3-BinA-PCR3_S121.yaml",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI0432CSXV/",
"accession": "IGVFFI0432CSXV",
"aliases": [
"jesse-engreitz:auxiliary_file_CRUDO_KITLG-Auxin0hrs-FF3-BinA-PCR2_S31"
],
"content_type": "reads",
"creation_timestamp": "2024-06-01T02:17:42.664333+00:00",
"file_format": "fastq",
"file_size": 15398250,
"href": "/sequence-files/IGVFFI0432CSXV/@@download/IGVFFI0432CSXV.fastq.gz",
"s3_uri": "s3://igvf-files/2024/06/01/61a0193f-b6c3-4298-9126-0859f2abe81e/IGVFFI0432CSXV.fastq.gz",
"sequencing_platform": "/platform-terms/EFO_0008565/",
"submitted_file_name": "/oak/stanford/groups/engreitz/Projects/Cohesin/220104B013_Cohesin_KITLG/fastq_trim/Auxin0hrs-FF3-BinA-PCR2_S31_R1_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI1136TXZO/",
"accession": "IGVFFI1136TXZO",
"aliases": [
"jesse-engreitz:auxiliary_file_CRUDO_KITLG-Auxin0hrs-FF3-BinA-PCR3_S121"
],
"content_type": "reads",
"creation_timestamp": "2024-06-01T02:18:00.689101+00:00",
"file_format": "fastq",
"file_size": 28321169,
"href": "/sequence-files/IGVFFI1136TXZO/@@download/IGVFFI1136TXZO.fastq.gz",
"s3_uri": "s3://igvf-files/2024/06/01/3c34e654-32d1-4d2f-b616-f7c13188fb68/IGVFFI1136TXZO.fastq.gz",
"sequencing_platform": "/platform-terms/EFO_0008565/",
"submitted_file_name": "/oak/stanford/groups/engreitz/Projects/Cohesin/220104B013_Cohesin_KITLG/fastq_trim/Auxin0hrs-FF3-BinA-PCR3_S121_R1_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/configuration-files/IGVFFI1197UKXM/",
"accession": "IGVFFI1197UKXM",
"aliases": [
"jesse-engreitz:seqspecfile_CRUDO_KITLG-Auxin0hrs-FF3-BinA-PCR4_S127"
],
"content_type": "seqspec",
"creation_timestamp": "2024-06-11T22:08:08.993736+00:00",
"file_format": "yaml",
"file_size": 904,
"href": "/configuration-files/IGVFFI1197UKXM/@@download/IGVFFI1197UKXM.yaml.gz",
"s3_uri": "s3://igvf-files/2024/06/11/361690bf-7953-4f06-b90c-58324f8ad591/IGVFFI1197UKXM.yaml.gz",
"submitted_file_name": "/oak/stanford/groups/engreitz/Projects/Cohesin/240410_IGVF_upload/seqspec/guideseq.out.Auxin0hrs-FF3-BinA-PCR4_S127.yaml",
"upload_status": "validated"
}
],
"input_file_set_for": [],
"lab": {
"@id": "/labs/jesse-engreitz/",
"title": "Jesse Engreitz, Stanford"
},
"measurement_sets": [
{
"@id": "/measurement-sets/IGVFDS4813YQOH/",
"accession": "IGVFDS4813YQOH",
"aliases": [
"jesse-engreitz:measurement_CRUDO_KITLG-Auxin0hrs-FF3-BinA-PCR1_S25",
"jesse-engreitz:measurement_CRUDO_KITLG-Auxin0hrs-FF3-BinA-PCR2_S31",
"jesse-engreitz:measurement_CRUDO_KITLG-Auxin0hrs-FF3-BinA-PCR3_S121",
"jesse-engreitz:measurement_CRUDO_KITLG-Auxin0hrs-FF3-BinA-PCR4_S127"
],
"preferred_assay_title": "CRISPR FlowFISH screen"
}
],
"release_timestamp": "2024-07-10T20:14:56.744157+00:00",
"samples": [
{
"@id": "/in-vitro-systems/IGVFSM2914OOTJ/",
"@type": [
"InVitroSystem",
"Biosample",
"Sample",
"Item"
],
"accession": "IGVFSM2914OOTJ",
"aliases": [
"jesse-engreitz:in-vitro-system_CRUDO_KITLG-Auxin0hrs-FF3-BinA-PCR1_S25",
"jesse-engreitz:in-vitro-system_CRUDO_KITLG-Auxin0hrs-FF3-BinA-PCR2_S31",
"jesse-engreitz:in-vitro-system_CRUDO_KITLG-Auxin0hrs-FF3-BinA-PCR3_S121",
"jesse-engreitz:in-vitro-system_CRUDO_KITLG-Auxin0hrs-FF3-BinA-PCR4_S127"
],
"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 A for 0-10% 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": "2024-06-01T02:17:25.198121+00:00",
"summary": "gRNA sequencing for CRISPR interference FlowFISH screen integrating a guide (sgRNA) library targeting accessible genome regions in many genomic loci",
"uuid": "9b8b011a-c5db-41ff-a42a-c54c22348f79"
}