{
"@context": "/terms/",
"@id": "/auxiliary-sets/IGVFDS8772YTOP/",
"@type": [
"AuxiliarySet",
"FileSet",
"Item"
],
"accession": "IGVFDS8772YTOP",
"aliases": [
"jesse-engreitz:auxiliary_CRUDO_KITLG-Auxin0hrs-FF1-BinF-PCR1_S6",
"jesse-engreitz:auxiliary_CRUDO_KITLG-Auxin0hrs-FF1-BinF-PCR2_S12",
"jesse-engreitz:auxiliary_CRUDO_KITLG-Auxin0hrs-FF1-BinF-PCR3_S102",
"jesse-engreitz:auxiliary_CRUDO_KITLG-Auxin0hrs-FF1-BinF-PCR4_S108"
],
"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 [IGVFDS8772YTOP](/auxiliary-sets/IGVFDS8772YTOP/) has sequence file(s) [IGVFFI6575LYZN](/sequence-files/IGVFFI6575LYZN/), [IGVFFI1910QCOP](/sequence-files/IGVFFI1910QCOP/), [IGVFFI7770QKUY](/sequence-files/IGVFFI7770QKUY/), [IGVFFI3880FPSK](/sequence-files/IGVFFI3880FPSK/) 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/IGVFDS8772YTOP/"
},
{
"category": "missing analysis",
"detail": "Auxiliary set [IGVFDS8772YTOP](/auxiliary-sets/IGVFDS8772YTOP/) 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/IGVFDS8772YTOP/"
}
]
},
"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": "2024-05-16T17:41:07.373627+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/IGVFFI6575LYZN/",
"accession": "IGVFFI6575LYZN",
"aliases": [
"jesse-engreitz:auxiliary_file_CRUDO_KITLG-Auxin0hrs-FF1-BinF-PCR1_S6"
],
"content_type": "reads",
"creation_timestamp": "2024-06-01T02:10:27.221651+00:00",
"file_format": "fastq",
"file_size": 20442777,
"href": "/sequence-files/IGVFFI6575LYZN/@@download/IGVFFI6575LYZN.fastq.gz",
"s3_uri": "s3://igvf-files/2024/06/01/b4defe1a-4c01-4616-8e48-91b24f734f41/IGVFFI6575LYZN.fastq.gz",
"sequencing_platform": "/platform-terms/EFO_0008565/",
"submitted_file_name": "/oak/stanford/groups/engreitz/Projects/Cohesin/220104B013_Cohesin_KITLG/fastq_trim/Auxin0hrs-FF1-BinF-PCR1_S6_R1_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/configuration-files/IGVFFI8582UZLK/",
"accession": "IGVFFI8582UZLK",
"aliases": [
"jesse-engreitz:seqspecfile_CRUDO_KITLG-Auxin0hrs-FF1-BinF-PCR1_S6"
],
"content_type": "seqspec",
"creation_timestamp": "2024-06-11T22:05:52.442076+00:00",
"file_format": "yaml",
"file_size": 902,
"href": "/configuration-files/IGVFFI8582UZLK/@@download/IGVFFI8582UZLK.yaml.gz",
"s3_uri": "s3://igvf-files/2024/06/11/6c4670fd-06f5-4a7f-910d-54b4d2073030/IGVFFI8582UZLK.yaml.gz",
"submitted_file_name": "/oak/stanford/groups/engreitz/Projects/Cohesin/240410_IGVF_upload/seqspec/guideseq.out.Auxin0hrs-FF1-BinF-PCR1_S6.yaml",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI1910QCOP/",
"accession": "IGVFFI1910QCOP",
"aliases": [
"jesse-engreitz:auxiliary_file_CRUDO_KITLG-Auxin0hrs-FF1-BinF-PCR3_S102"
],
"content_type": "reads",
"creation_timestamp": "2024-06-01T02:11:07.268875+00:00",
"file_format": "fastq",
"file_size": 38522468,
"href": "/sequence-files/IGVFFI1910QCOP/@@download/IGVFFI1910QCOP.fastq.gz",
"s3_uri": "s3://igvf-files/2024/06/01/48867b74-44ca-4b5f-9fa7-9f99164aa891/IGVFFI1910QCOP.fastq.gz",
"sequencing_platform": "/platform-terms/EFO_0008565/",
"submitted_file_name": "/oak/stanford/groups/engreitz/Projects/Cohesin/220104B013_Cohesin_KITLG/fastq_trim/Auxin0hrs-FF1-BinF-PCR3_S102_R1_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI7770QKUY/",
"accession": "IGVFFI7770QKUY",
"aliases": [
"jesse-engreitz:auxiliary_file_CRUDO_KITLG-Auxin0hrs-FF1-BinF-PCR4_S108"
],
"content_type": "reads",
"creation_timestamp": "2024-06-01T02:14:26.364740+00:00",
"file_format": "fastq",
"file_size": 44307926,
"href": "/sequence-files/IGVFFI7770QKUY/@@download/IGVFFI7770QKUY.fastq.gz",
"s3_uri": "s3://igvf-files/2024/06/01/8bcdf0c8-2be2-446e-9da5-86b984d2db15/IGVFFI7770QKUY.fastq.gz",
"sequencing_platform": "/platform-terms/EFO_0008565/",
"submitted_file_name": "/oak/stanford/groups/engreitz/Projects/Cohesin/220104B013_Cohesin_KITLG/fastq_trim/Auxin0hrs-FF1-BinF-PCR4_S108_R1_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI3880FPSK/",
"accession": "IGVFFI3880FPSK",
"aliases": [
"jesse-engreitz:auxiliary_file_CRUDO_KITLG-Auxin0hrs-FF1-BinF-PCR2_S12"
],
"content_type": "reads",
"creation_timestamp": "2024-06-01T02:10:49.254748+00:00",
"file_format": "fastq",
"file_size": 15427391,
"href": "/sequence-files/IGVFFI3880FPSK/@@download/IGVFFI3880FPSK.fastq.gz",
"s3_uri": "s3://igvf-files/2024/06/01/a8376b5f-7bb3-439a-b441-8ab5607abb3d/IGVFFI3880FPSK.fastq.gz",
"sequencing_platform": "/platform-terms/EFO_0008565/",
"submitted_file_name": "/oak/stanford/groups/engreitz/Projects/Cohesin/220104B013_Cohesin_KITLG/fastq_trim/Auxin0hrs-FF1-BinF-PCR2_S12_R1_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/configuration-files/IGVFFI1199IUIN/",
"accession": "IGVFFI1199IUIN",
"aliases": [
"jesse-engreitz:seqspecfile_CRUDO_KITLG-Auxin0hrs-FF1-BinF-PCR2_S12"
],
"content_type": "seqspec",
"creation_timestamp": "2024-06-11T22:06:05.952559+00:00",
"file_format": "yaml",
"file_size": 901,
"href": "/configuration-files/IGVFFI1199IUIN/@@download/IGVFFI1199IUIN.yaml.gz",
"s3_uri": "s3://igvf-files/2024/06/11/29d519de-2697-4f9f-92c6-a47dce07add3/IGVFFI1199IUIN.yaml.gz",
"submitted_file_name": "/oak/stanford/groups/engreitz/Projects/Cohesin/240410_IGVF_upload/seqspec/guideseq.out.Auxin0hrs-FF1-BinF-PCR2_S12.yaml",
"upload_status": "validated"
},
{
"@id": "/configuration-files/IGVFFI0059WNTR/",
"accession": "IGVFFI0059WNTR",
"aliases": [
"jesse-engreitz:seqspecfile_CRUDO_KITLG-Auxin0hrs-FF1-BinF-PCR3_S102"
],
"content_type": "seqspec",
"creation_timestamp": "2024-06-11T22:06:19.359333+00:00",
"file_format": "yaml",
"file_size": 902,
"href": "/configuration-files/IGVFFI0059WNTR/@@download/IGVFFI0059WNTR.yaml.gz",
"s3_uri": "s3://igvf-files/2024/06/11/2b61137f-8665-44a6-abec-7caeba4b818d/IGVFFI0059WNTR.yaml.gz",
"submitted_file_name": "/oak/stanford/groups/engreitz/Projects/Cohesin/240410_IGVF_upload/seqspec/guideseq.out.Auxin0hrs-FF1-BinF-PCR3_S102.yaml",
"upload_status": "validated"
},
{
"@id": "/configuration-files/IGVFFI7676KGCV/",
"accession": "IGVFFI7676KGCV",
"aliases": [
"jesse-engreitz:seqspecfile_CRUDO_KITLG-Auxin0hrs-FF1-BinF-PCR4_S108"
],
"content_type": "seqspec",
"creation_timestamp": "2024-06-11T22:06:32.856796+00:00",
"file_format": "yaml",
"file_size": 904,
"href": "/configuration-files/IGVFFI7676KGCV/@@download/IGVFFI7676KGCV.yaml.gz",
"s3_uri": "s3://igvf-files/2024/06/11/5e09aac3-5770-4ca0-bcc4-ed52f679cb30/IGVFFI7676KGCV.yaml.gz",
"submitted_file_name": "/oak/stanford/groups/engreitz/Projects/Cohesin/240410_IGVF_upload/seqspec/guideseq.out.Auxin0hrs-FF1-BinF-PCR4_S108.yaml",
"upload_status": "validated"
}
],
"input_file_set_for": [],
"lab": {
"@id": "/labs/jesse-engreitz/",
"title": "Jesse Engreitz, Stanford"
},
"measurement_sets": [
{
"@id": "/measurement-sets/IGVFDS7789CCCR/",
"accession": "IGVFDS7789CCCR",
"aliases": [
"jesse-engreitz:measurement_CRUDO_KITLG-Auxin0hrs-FF1-BinF-PCR1_S6",
"jesse-engreitz:measurement_CRUDO_KITLG-Auxin0hrs-FF1-BinF-PCR2_S12",
"jesse-engreitz:measurement_CRUDO_KITLG-Auxin0hrs-FF1-BinF-PCR3_S102",
"jesse-engreitz:measurement_CRUDO_KITLG-Auxin0hrs-FF1-BinF-PCR4_S108"
],
"preferred_assay_title": "CRISPR FlowFISH screen"
}
],
"release_timestamp": "2024-07-10T20:14:06.047463+00:00",
"samples": [
{
"@id": "/in-vitro-systems/IGVFSM9117BTSA/",
"@type": [
"InVitroSystem",
"Biosample",
"Sample",
"Item"
],
"accession": "IGVFSM9117BTSA",
"aliases": [
"jesse-engreitz:in-vitro-system_CRUDO_KITLG-Auxin0hrs-FF1-BinF-PCR1_S6",
"jesse-engreitz:in-vitro-system_CRUDO_KITLG-Auxin0hrs-FF1-BinF-PCR2_S12",
"jesse-engreitz:in-vitro-system_CRUDO_KITLG-Auxin0hrs-FF1-BinF-PCR3_S102",
"jesse-engreitz:in-vitro-system_CRUDO_KITLG-Auxin0hrs-FF1-BinF-PCR4_S108"
],
"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 F for 80-100% 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": "2024-06-01T02:10:27.221651+00:00",
"summary": "gRNA sequencing for CRISPR interference FlowFISH screen integrating a guide (sgRNA) library targeting accessible genome regions in many genomic loci",
"uuid": "3941d1f1-bdc9-4966-bb87-beba3b801cf4"
}