{
"@context": "/terms/",
"@id": "/auxiliary-sets/IGVFDS7634SPOA/",
"@type": [
"AuxiliarySet",
"FileSet",
"Item"
],
"accession": "IGVFDS7634SPOA",
"aliases": [
"jesse-engreitz:auxiliary_CRUDO_MYC-Auxin0hrs-FF1-BinD-PCR1_Rep1_S4",
"jesse-engreitz:auxiliary_CRUDO_MYC-Auxin0hrs-FF1-BinD-PCR1_Rep2_S59",
"jesse-engreitz:auxiliary_CRUDO_MYC-Auxin0hrs-FF1-BinD-PCR2_Rep1_S10",
"jesse-engreitz:auxiliary_CRUDO_MYC-Auxin0hrs-FF1-BinD-PCR2_Rep2_S65",
"jesse-engreitz:auxiliary_CRUDO_MYC-Auxin0hrs-FF1-BinD-PCR3_Rep1_S16",
"jesse-engreitz:auxiliary_CRUDO_MYC-Auxin0hrs-FF1-BinD-PCR3_Rep2_S71",
"jesse-engreitz:auxiliary_CRUDO_MYC-Auxin0hrs-FF1-BinD-PCR4_Rep1_S22",
"jesse-engreitz:auxiliary_CRUDO_MYC-Auxin0hrs-FF1-BinD-PCR4_Rep2_S77"
],
"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 [IGVFDS7634SPOA](/auxiliary-sets/IGVFDS7634SPOA/) has sequence file(s) [IGVFFI6727EKGM](/sequence-files/IGVFFI6727EKGM/), [IGVFFI9320EENZ](/sequence-files/IGVFFI9320EENZ/), [IGVFFI3107NMCV](/sequence-files/IGVFFI3107NMCV/), [IGVFFI2143VXMF](/sequence-files/IGVFFI2143VXMF/), [IGVFFI3177EXCB](/sequence-files/IGVFFI3177EXCB/), [IGVFFI4680QVWM](/sequence-files/IGVFFI4680QVWM/), [IGVFFI8552NKOB](/sequence-files/IGVFFI8552NKOB/), [IGVFFI0342EICI](/sequence-files/IGVFFI0342EICI/) 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/IGVFDS7634SPOA/"
},
{
"category": "missing analysis",
"detail": "Auxiliary set [IGVFDS7634SPOA](/auxiliary-sets/IGVFDS7634SPOA/) 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/IGVFDS7634SPOA/"
}
]
},
"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": "2024-05-21T17:12:25.497716+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/IGVFFI6727EKGM/",
"accession": "IGVFFI6727EKGM",
"aliases": [
"jesse-engreitz:auxiliary_file_CRUDO_MYC-Auxin0hrs-FF1-BinD-PCR1_Rep1_S4"
],
"content_type": "reads",
"creation_timestamp": "2024-06-01T01:58:10.657499+00:00",
"file_format": "fastq",
"file_size": 34230112,
"href": "/sequence-files/IGVFFI6727EKGM/@@download/IGVFFI6727EKGM.fastq.gz",
"s3_uri": "s3://igvf-files/2024/06/01/1cb5cc53-dc0a-4b4d-99c7-4f6f96063e81/IGVFFI6727EKGM.fastq.gz",
"sequencing_platform": "/platform-terms/EFO_0008565/",
"submitted_file_name": "/oak/stanford/groups/engreitz/Projects/Cohesin/220819B015_MYC/fastq_trim/MYC-Auxin0hrs-FF1-BinD-PCR1-Rep1_S4_R1_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/configuration-files/IGVFFI2607QYLY/",
"accession": "IGVFFI2607QYLY",
"aliases": [
"jesse-engreitz:seqspecfile_CRUDO_MYC-Auxin0hrs-FF1-BinD-PCR1_Rep1_S4"
],
"content_type": "seqspec",
"creation_timestamp": "2024-06-11T20:45:40.425915+00:00",
"file_format": "yaml",
"file_size": 909,
"href": "/configuration-files/IGVFFI2607QYLY/@@download/IGVFFI2607QYLY.yaml.gz",
"s3_uri": "s3://igvf-files/2024/06/11/8c5f6b86-7ab2-4355-a949-f8feb3d44074/IGVFFI2607QYLY.yaml.gz",
"submitted_file_name": "/oak/stanford/groups/engreitz/Projects/Cohesin/240410_IGVF_upload/seqspec/guideseq.out.MYC-Auxin0hrs-FF1-BinD-PCR1_Rep1_S4.yaml",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI9320EENZ/",
"accession": "IGVFFI9320EENZ",
"aliases": [
"jesse-engreitz:auxiliary_file_CRUDO_MYC-Auxin0hrs-FF1-BinD-PCR2_Rep1_S10"
],
"content_type": "reads",
"creation_timestamp": "2024-06-01T01:58:50.554639+00:00",
"file_format": "fastq",
"file_size": 29331280,
"href": "/sequence-files/IGVFFI9320EENZ/@@download/IGVFFI9320EENZ.fastq.gz",
"s3_uri": "s3://igvf-files/2024/06/01/60f90cdb-83cc-4587-8cf5-7c7275016f87/IGVFFI9320EENZ.fastq.gz",
"sequencing_platform": "/platform-terms/EFO_0008565/",
"submitted_file_name": "/oak/stanford/groups/engreitz/Projects/Cohesin/220819B015_MYC/fastq_trim/MYC-Auxin0hrs-FF1-BinD-PCR2-Rep1_S10_R1_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/configuration-files/IGVFFI6755HBWI/",
"accession": "IGVFFI6755HBWI",
"aliases": [
"jesse-engreitz:seqspecfile_CRUDO_MYC-Auxin0hrs-FF1-BinD-PCR3_Rep2_S71"
],
"content_type": "seqspec",
"creation_timestamp": "2024-06-11T20:46:49.843394+00:00",
"file_format": "yaml",
"file_size": 910,
"href": "/configuration-files/IGVFFI6755HBWI/@@download/IGVFFI6755HBWI.yaml.gz",
"s3_uri": "s3://igvf-files/2024/06/11/ebcc9f86-23e2-4e48-a16e-51880c648761/IGVFFI6755HBWI.yaml.gz",
"submitted_file_name": "/oak/stanford/groups/engreitz/Projects/Cohesin/240410_IGVF_upload/seqspec/guideseq.out.MYC-Auxin0hrs-FF1-BinD-PCR3_Rep2_S71.yaml",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI3107NMCV/",
"accession": "IGVFFI3107NMCV",
"aliases": [
"jesse-engreitz:auxiliary_file_CRUDO_MYC-Auxin0hrs-FF1-BinD-PCR3_Rep1_S16"
],
"content_type": "reads",
"creation_timestamp": "2024-06-01T01:59:32.059778+00:00",
"file_format": "fastq",
"file_size": 39537629,
"href": "/sequence-files/IGVFFI3107NMCV/@@download/IGVFFI3107NMCV.fastq.gz",
"s3_uri": "s3://igvf-files/2024/06/01/6b4a9c21-66df-483c-9722-1a964880a763/IGVFFI3107NMCV.fastq.gz",
"sequencing_platform": "/platform-terms/EFO_0008565/",
"submitted_file_name": "/oak/stanford/groups/engreitz/Projects/Cohesin/220819B015_MYC/fastq_trim/MYC-Auxin0hrs-FF1-BinD-PCR3-Rep1_S16_R1_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/configuration-files/IGVFFI3508KOBE/",
"accession": "IGVFFI3508KOBE",
"aliases": [
"jesse-engreitz:seqspecfile_CRUDO_MYC-Auxin0hrs-FF1-BinD-PCR4_Rep2_S77"
],
"content_type": "seqspec",
"creation_timestamp": "2024-06-11T20:47:17.823558+00:00",
"file_format": "yaml",
"file_size": 911,
"href": "/configuration-files/IGVFFI3508KOBE/@@download/IGVFFI3508KOBE.yaml.gz",
"s3_uri": "s3://igvf-files/2024/06/11/c02754bc-f558-449d-938a-a2582d1e40e2/IGVFFI3508KOBE.yaml.gz",
"submitted_file_name": "/oak/stanford/groups/engreitz/Projects/Cohesin/240410_IGVF_upload/seqspec/guideseq.out.MYC-Auxin0hrs-FF1-BinD-PCR4_Rep2_S77.yaml",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI2143VXMF/",
"accession": "IGVFFI2143VXMF",
"aliases": [
"jesse-engreitz:auxiliary_file_CRUDO_MYC-Auxin0hrs-FF1-BinD-PCR4_Rep1_S22"
],
"content_type": "reads",
"creation_timestamp": "2024-06-01T02:00:13.449316+00:00",
"file_format": "fastq",
"file_size": 39517519,
"href": "/sequence-files/IGVFFI2143VXMF/@@download/IGVFFI2143VXMF.fastq.gz",
"s3_uri": "s3://igvf-files/2024/06/01/fca26270-f5dc-4e62-bea0-8eb3daa1dde3/IGVFFI2143VXMF.fastq.gz",
"sequencing_platform": "/platform-terms/EFO_0008565/",
"submitted_file_name": "/oak/stanford/groups/engreitz/Projects/Cohesin/220819B015_MYC/fastq_trim/MYC-Auxin0hrs-FF1-BinD-PCR4-Rep1_S22_R1_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI3177EXCB/",
"accession": "IGVFFI3177EXCB",
"aliases": [
"jesse-engreitz:auxiliary_file_CRUDO_MYC-Auxin0hrs-FF1-BinD-PCR4_Rep2_S77"
],
"content_type": "reads",
"creation_timestamp": "2024-06-01T02:00:34.588190+00:00",
"file_format": "fastq",
"file_size": 20207838,
"href": "/sequence-files/IGVFFI3177EXCB/@@download/IGVFFI3177EXCB.fastq.gz",
"s3_uri": "s3://igvf-files/2024/06/01/9fbaf1ac-51f4-4aa0-92e0-2e705752814e/IGVFFI3177EXCB.fastq.gz",
"sequencing_platform": "/platform-terms/EFO_0008565/",
"submitted_file_name": "/oak/stanford/groups/engreitz/Projects/Cohesin/220819B015_MYC/fastq_trim/MYC-Auxin0hrs-FF1-BinD-PCR4-Rep2_S77_R1_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI4680QVWM/",
"accession": "IGVFFI4680QVWM",
"aliases": [
"jesse-engreitz:auxiliary_file_CRUDO_MYC-Auxin0hrs-FF1-BinD-PCR1_Rep2_S59"
],
"content_type": "reads",
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"file_format": "fastq",
"file_size": 17731219,
"href": "/sequence-files/IGVFFI4680QVWM/@@download/IGVFFI4680QVWM.fastq.gz",
"s3_uri": "s3://igvf-files/2024/06/01/84d6b732-f874-4485-ba54-9de99eff3c9e/IGVFFI4680QVWM.fastq.gz",
"sequencing_platform": "/platform-terms/EFO_0008565/",
"submitted_file_name": "/oak/stanford/groups/engreitz/Projects/Cohesin/220819B015_MYC/fastq_trim/MYC-Auxin0hrs-FF1-BinD-PCR1-Rep2_S59_R1_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI8552NKOB/",
"accession": "IGVFFI8552NKOB",
"aliases": [
"jesse-engreitz:auxiliary_file_CRUDO_MYC-Auxin0hrs-FF1-BinD-PCR2_Rep2_S65"
],
"content_type": "reads",
"creation_timestamp": "2024-06-01T01:59:12.982173+00:00",
"file_format": "fastq",
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"href": "/sequence-files/IGVFFI8552NKOB/@@download/IGVFFI8552NKOB.fastq.gz",
"s3_uri": "s3://igvf-files/2024/06/01/da39e7a4-f793-41a3-a510-adf485077fc1/IGVFFI8552NKOB.fastq.gz",
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"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI0342EICI/",
"accession": "IGVFFI0342EICI",
"aliases": [
"jesse-engreitz:auxiliary_file_CRUDO_MYC-Auxin0hrs-FF1-BinD-PCR3_Rep2_S71"
],
"content_type": "reads",
"creation_timestamp": "2024-06-01T01:59:53.306769+00:00",
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"href": "/sequence-files/IGVFFI0342EICI/@@download/IGVFFI0342EICI.fastq.gz",
"s3_uri": "s3://igvf-files/2024/06/01/44e4f2e0-a40d-480b-b81e-9a17346ea73c/IGVFFI0342EICI.fastq.gz",
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"upload_status": "validated"
},
{
"@id": "/configuration-files/IGVFFI4180WBMT/",
"accession": "IGVFFI4180WBMT",
"aliases": [
"jesse-engreitz:seqspecfile_CRUDO_MYC-Auxin0hrs-FF1-BinD-PCR2_Rep2_S65"
],
"content_type": "seqspec",
"creation_timestamp": "2024-06-11T20:46:20.996077+00:00",
"file_format": "yaml",
"file_size": 911,
"href": "/configuration-files/IGVFFI4180WBMT/@@download/IGVFFI4180WBMT.yaml.gz",
"s3_uri": "s3://igvf-files/2024/06/11/74e9150a-949b-4941-90ee-9a0c9ef29d75/IGVFFI4180WBMT.yaml.gz",
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"upload_status": "validated"
},
{
"@id": "/configuration-files/IGVFFI0710SHET/",
"accession": "IGVFFI0710SHET",
"aliases": [
"jesse-engreitz:seqspecfile_CRUDO_MYC-Auxin0hrs-FF1-BinD-PCR4_Rep1_S22"
],
"content_type": "seqspec",
"creation_timestamp": "2024-06-11T20:47:03.806781+00:00",
"file_format": "yaml",
"file_size": 911,
"href": "/configuration-files/IGVFFI0710SHET/@@download/IGVFFI0710SHET.yaml.gz",
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"upload_status": "validated"
},
{
"@id": "/configuration-files/IGVFFI0808YUDW/",
"accession": "IGVFFI0808YUDW",
"aliases": [
"jesse-engreitz:seqspecfile_CRUDO_MYC-Auxin0hrs-FF1-BinD-PCR1_Rep2_S59"
],
"content_type": "seqspec",
"creation_timestamp": "2024-06-11T20:45:54.049564+00:00",
"file_format": "yaml",
"file_size": 911,
"href": "/configuration-files/IGVFFI0808YUDW/@@download/IGVFFI0808YUDW.yaml.gz",
"s3_uri": "s3://igvf-files/2024/06/11/d67a15b0-a2dd-48a1-aa0e-74e07f04a05f/IGVFFI0808YUDW.yaml.gz",
"submitted_file_name": "/oak/stanford/groups/engreitz/Projects/Cohesin/240410_IGVF_upload/seqspec/guideseq.out.MYC-Auxin0hrs-FF1-BinD-PCR1_Rep2_S59.yaml",
"upload_status": "validated"
},
{
"@id": "/configuration-files/IGVFFI5598HNTC/",
"accession": "IGVFFI5598HNTC",
"aliases": [
"jesse-engreitz:seqspecfile_CRUDO_MYC-Auxin0hrs-FF1-BinD-PCR2_Rep1_S10"
],
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"file_format": "yaml",
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"href": "/configuration-files/IGVFFI5598HNTC/@@download/IGVFFI5598HNTC.yaml.gz",
"s3_uri": "s3://igvf-files/2024/06/11/1126dbf8-0491-4558-930a-5eba15d17532/IGVFFI5598HNTC.yaml.gz",
"submitted_file_name": "/oak/stanford/groups/engreitz/Projects/Cohesin/240410_IGVF_upload/seqspec/guideseq.out.MYC-Auxin0hrs-FF1-BinD-PCR2_Rep1_S10.yaml",
"upload_status": "validated"
},
{
"@id": "/configuration-files/IGVFFI5922AKJR/",
"accession": "IGVFFI5922AKJR",
"aliases": [
"jesse-engreitz:seqspecfile_CRUDO_MYC-Auxin0hrs-FF1-BinD-PCR3_Rep1_S16"
],
"content_type": "seqspec",
"creation_timestamp": "2024-06-11T20:46:35.817266+00:00",
"file_format": "yaml",
"file_size": 910,
"href": "/configuration-files/IGVFFI5922AKJR/@@download/IGVFFI5922AKJR.yaml.gz",
"s3_uri": "s3://igvf-files/2024/06/11/155572f8-a580-4d39-9c26-435339eb6575/IGVFFI5922AKJR.yaml.gz",
"submitted_file_name": "/oak/stanford/groups/engreitz/Projects/Cohesin/240410_IGVF_upload/seqspec/guideseq.out.MYC-Auxin0hrs-FF1-BinD-PCR3_Rep1_S16.yaml",
"upload_status": "validated"
}
],
"input_file_set_for": [],
"lab": {
"@id": "/labs/jesse-engreitz/",
"title": "Jesse Engreitz, Stanford"
},
"measurement_sets": [
{
"@id": "/measurement-sets/IGVFDS7409OQIL/",
"accession": "IGVFDS7409OQIL",
"aliases": [
"jesse-engreitz:measurement_CRUDO_MYC-Auxin0hrs-FF1-BinD-PCR1_Rep1_S4",
"jesse-engreitz:measurement_CRUDO_MYC-Auxin0hrs-FF1-BinD-PCR1_Rep2_S59",
"jesse-engreitz:measurement_CRUDO_MYC-Auxin0hrs-FF1-BinD-PCR2_Rep1_S10",
"jesse-engreitz:measurement_CRUDO_MYC-Auxin0hrs-FF1-BinD-PCR2_Rep2_S65",
"jesse-engreitz:measurement_CRUDO_MYC-Auxin0hrs-FF1-BinD-PCR3_Rep1_S16",
"jesse-engreitz:measurement_CRUDO_MYC-Auxin0hrs-FF1-BinD-PCR3_Rep2_S71",
"jesse-engreitz:measurement_CRUDO_MYC-Auxin0hrs-FF1-BinD-PCR4_Rep1_S22",
"jesse-engreitz:measurement_CRUDO_MYC-Auxin0hrs-FF1-BinD-PCR4_Rep2_S77"
],
"preferred_assay_title": "CRISPR FlowFISH screen"
}
],
"release_timestamp": "2024-07-10T20:19:36.505369+00:00",
"samples": [
{
"@id": "/in-vitro-systems/IGVFSM0111NTPA/",
"@type": [
"InVitroSystem",
"Biosample",
"Sample",
"Item"
],
"accession": "IGVFSM0111NTPA",
"aliases": [
"jesse-engreitz:in-vitro-system_CRUDO_MYC-Auxin0hrs-FF1-BinD-PCR1_Rep1_S4",
"jesse-engreitz:in-vitro-system_CRUDO_MYC-Auxin0hrs-FF1-BinD-PCR1_Rep2_S59",
"jesse-engreitz:in-vitro-system_CRUDO_MYC-Auxin0hrs-FF1-BinD-PCR2_Rep1_S10",
"jesse-engreitz:in-vitro-system_CRUDO_MYC-Auxin0hrs-FF1-BinD-PCR2_Rep2_S65",
"jesse-engreitz:in-vitro-system_CRUDO_MYC-Auxin0hrs-FF1-BinD-PCR3_Rep1_S16",
"jesse-engreitz:in-vitro-system_CRUDO_MYC-Auxin0hrs-FF1-BinD-PCR3_Rep2_S71",
"jesse-engreitz:in-vitro-system_CRUDO_MYC-Auxin0hrs-FF1-BinD-PCR4_Rep1_S22",
"jesse-engreitz:in-vitro-system_CRUDO_MYC-Auxin0hrs-FF1-BinD-PCR4_Rep2_S77"
],
"classifications": [
"cell line"
],
"construct_library_sets": [
"/construct-library-sets/IGVFDS7857SYCK/"
],
"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 MYC) 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": "2024-06-01T01:58:10.657499+00:00",
"summary": "gRNA sequencing for CRISPR interference FlowFISH screen integrating a guide (sgRNA) library targeting accessible genome regions in many genomic loci",
"uuid": "8f2272dd-5bd6-402e-b785-4b539dade3cd"
}