{
"@context": "/terms/",
"@id": "/auxiliary-sets/IGVFDS7919SMDO/",
"@type": [
"AuxiliarySet",
"FileSet",
"Item"
],
"accession": "IGVFDS7919SMDO",
"aliases": [
"jesse-engreitz:auxiliary_CRUDO_FAM3C_Auxin0hrs-FF1-BinC-PCR1-Rep1_S111",
"jesse-engreitz:auxiliary_CRUDO_FAM3C_Auxin0hrs-FF1-BinC-PCR2-Rep1_S117",
"jesse-engreitz:auxiliary_CRUDO_FAM3C_Auxin0hrs-FF1-BinC-PCR3-Rep1_S165",
"jesse-engreitz:auxiliary_CRUDO_FAM3C_Auxin0hrs-FF1-BinC-PCR4-Rep1_S171"
],
"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 [IGVFDS7919SMDO](/auxiliary-sets/IGVFDS7919SMDO/) has sequence file(s) [IGVFFI8872NVWQ](/sequence-files/IGVFFI8872NVWQ/), [IGVFFI0344PKCL](/sequence-files/IGVFFI0344PKCL/), [IGVFFI3522NTQE](/sequence-files/IGVFFI3522NTQE/), [IGVFFI1935HBGJ](/sequence-files/IGVFFI1935HBGJ/) 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/IGVFDS7919SMDO/"
},
{
"category": "missing analysis",
"detail": "Auxiliary set [IGVFDS7919SMDO](/auxiliary-sets/IGVFDS7919SMDO/) 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/IGVFDS7919SMDO/"
}
]
},
"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": "2024-05-14T16:23:52.239982+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/IGVFFI8872NVWQ/",
"accession": "IGVFFI8872NVWQ",
"aliases": [
"jesse-engreitz:auxiliary_file_CRUDO_FAM3C_Auxin0hrs-FF1-BinC-PCR1-Rep1_S111"
],
"content_type": "reads",
"creation_timestamp": "2024-06-01T01:50:56.162564+00:00",
"file_format": "fastq",
"file_size": 30443401,
"href": "/sequence-files/IGVFFI8872NVWQ/@@download/IGVFFI8872NVWQ.fastq.gz",
"s3_uri": "s3://igvf-files/2024/06/01/46cbe9f1-75f4-406e-ac25-f772debd33b8/IGVFFI8872NVWQ.fastq.gz",
"sequencing_platform": "/platform-terms/EFO_0008565/",
"submitted_file_name": "/oak/stanford/groups/engreitz/Projects/Cohesin/220308B014_CCND1_SSFA2_FAM3C/fastq_trim/FAM3C-Auxin0hrs-FF1-BinC-PCR1-Rep1_S111_R1_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/configuration-files/IGVFFI3708LBFB/",
"accession": "IGVFFI3708LBFB",
"aliases": [
"jesse-engreitz:seqspecfile_CRUDO_FAM3C_Auxin0hrs-FF1-BinC-PCR1-Rep1_S111"
],
"content_type": "seqspec",
"creation_timestamp": "2024-06-11T20:41:54.634793+00:00",
"file_format": "yaml",
"file_size": 914,
"href": "/configuration-files/IGVFFI3708LBFB/@@download/IGVFFI3708LBFB.yaml.gz",
"s3_uri": "s3://igvf-files/2024/06/11/813e5f29-e3ed-491c-9f88-25d059eba0f0/IGVFFI3708LBFB.yaml.gz",
"submitted_file_name": "/oak/stanford/groups/engreitz/Projects/Cohesin/240410_IGVF_upload/seqspec/guideseq.out.FAM3C_Auxin0hrs-FF1-BinC-PCR1-Rep1_S111.yaml",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI0344PKCL/",
"accession": "IGVFFI0344PKCL",
"aliases": [
"jesse-engreitz:auxiliary_file_CRUDO_FAM3C_Auxin0hrs-FF1-BinC-PCR2-Rep1_S117"
],
"content_type": "reads",
"creation_timestamp": "2024-06-01T01:51:16.436362+00:00",
"file_format": "fastq",
"file_size": 30407619,
"href": "/sequence-files/IGVFFI0344PKCL/@@download/IGVFFI0344PKCL.fastq.gz",
"s3_uri": "s3://igvf-files/2024/06/01/d8975246-beb5-4cf6-82f9-b26d4f07cc27/IGVFFI0344PKCL.fastq.gz",
"sequencing_platform": "/platform-terms/EFO_0008565/",
"submitted_file_name": "/oak/stanford/groups/engreitz/Projects/Cohesin/220308B014_CCND1_SSFA2_FAM3C/fastq_trim/FAM3C-Auxin0hrs-FF1-BinC-PCR2-Rep1_S117_R1_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI3522NTQE/",
"accession": "IGVFFI3522NTQE",
"aliases": [
"jesse-engreitz:auxiliary_file_CRUDO_FAM3C_Auxin0hrs-FF1-BinC-PCR3-Rep1_S165"
],
"content_type": "reads",
"creation_timestamp": "2024-06-01T01:51:34.711164+00:00",
"file_format": "fastq",
"file_size": 33732788,
"href": "/sequence-files/IGVFFI3522NTQE/@@download/IGVFFI3522NTQE.fastq.gz",
"s3_uri": "s3://igvf-files/2024/06/01/2a881543-ae33-40a6-b3b9-bf6b05789a5b/IGVFFI3522NTQE.fastq.gz",
"sequencing_platform": "/platform-terms/EFO_0008565/",
"submitted_file_name": "/oak/stanford/groups/engreitz/Projects/Cohesin/220308B014_CCND1_SSFA2_FAM3C/fastq_trim/FAM3C-Auxin0hrs-FF1-BinC-PCR3-Rep1_S165_R1_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI1935HBGJ/",
"accession": "IGVFFI1935HBGJ",
"aliases": [
"jesse-engreitz:auxiliary_file_CRUDO_FAM3C_Auxin0hrs-FF1-BinC-PCR4-Rep1_S171"
],
"content_type": "reads",
"creation_timestamp": "2024-06-01T01:51:54.383927+00:00",
"file_format": "fastq",
"file_size": 31253134,
"href": "/sequence-files/IGVFFI1935HBGJ/@@download/IGVFFI1935HBGJ.fastq.gz",
"s3_uri": "s3://igvf-files/2024/06/01/17f46a2e-72cd-43a9-8467-12760dad5204/IGVFFI1935HBGJ.fastq.gz",
"sequencing_platform": "/platform-terms/EFO_0008565/",
"submitted_file_name": "/oak/stanford/groups/engreitz/Projects/Cohesin/220308B014_CCND1_SSFA2_FAM3C/fastq_trim/FAM3C-Auxin0hrs-FF1-BinC-PCR4-Rep1_S171_R1_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/configuration-files/IGVFFI9742OJPT/",
"accession": "IGVFFI9742OJPT",
"aliases": [
"jesse-engreitz:seqspecfile_CRUDO_FAM3C_Auxin0hrs-FF1-BinC-PCR3-Rep1_S165"
],
"content_type": "seqspec",
"creation_timestamp": "2024-06-11T20:42:24.320217+00:00",
"file_format": "yaml",
"file_size": 913,
"href": "/configuration-files/IGVFFI9742OJPT/@@download/IGVFFI9742OJPT.yaml.gz",
"s3_uri": "s3://igvf-files/2024/06/11/ccf9f163-167f-4944-9462-3dfb0fc22d82/IGVFFI9742OJPT.yaml.gz",
"submitted_file_name": "/oak/stanford/groups/engreitz/Projects/Cohesin/240410_IGVF_upload/seqspec/guideseq.out.FAM3C_Auxin0hrs-FF1-BinC-PCR3-Rep1_S165.yaml",
"upload_status": "validated"
},
{
"@id": "/configuration-files/IGVFFI1431QPOY/",
"accession": "IGVFFI1431QPOY",
"aliases": [
"jesse-engreitz:seqspecfile_CRUDO_FAM3C_Auxin0hrs-FF1-BinC-PCR2-Rep1_S117"
],
"content_type": "seqspec",
"creation_timestamp": "2024-06-11T20:42:10.055415+00:00",
"file_format": "yaml",
"file_size": 913,
"href": "/configuration-files/IGVFFI1431QPOY/@@download/IGVFFI1431QPOY.yaml.gz",
"s3_uri": "s3://igvf-files/2024/06/11/056bbf36-1e2d-4c0f-a887-221e342825ec/IGVFFI1431QPOY.yaml.gz",
"submitted_file_name": "/oak/stanford/groups/engreitz/Projects/Cohesin/240410_IGVF_upload/seqspec/guideseq.out.FAM3C_Auxin0hrs-FF1-BinC-PCR2-Rep1_S117.yaml",
"upload_status": "validated"
},
{
"@id": "/configuration-files/IGVFFI0260NNBS/",
"accession": "IGVFFI0260NNBS",
"aliases": [
"jesse-engreitz:seqspecfile_CRUDO_FAM3C_Auxin0hrs-FF1-BinC-PCR4-Rep1_S171"
],
"content_type": "seqspec",
"creation_timestamp": "2024-06-11T20:42:37.514366+00:00",
"file_format": "yaml",
"file_size": 913,
"href": "/configuration-files/IGVFFI0260NNBS/@@download/IGVFFI0260NNBS.yaml.gz",
"s3_uri": "s3://igvf-files/2024/06/11/5058b3d1-6aec-4743-a742-dd747c69f3f0/IGVFFI0260NNBS.yaml.gz",
"submitted_file_name": "/oak/stanford/groups/engreitz/Projects/Cohesin/240410_IGVF_upload/seqspec/guideseq.out.FAM3C_Auxin0hrs-FF1-BinC-PCR4-Rep1_S171.yaml",
"upload_status": "validated"
}
],
"input_file_set_for": [],
"lab": {
"@id": "/labs/jesse-engreitz/",
"title": "Jesse Engreitz, Stanford"
},
"measurement_sets": [
{
"@id": "/measurement-sets/IGVFDS5285ESHJ/",
"accession": "IGVFDS5285ESHJ",
"aliases": [
"jesse-engreitz:measurement_CRUDO_FAM3C_Auxin0hrs-FF1-BinC-PCR1-Rep1_S111",
"jesse-engreitz:measurement_CRUDO_FAM3C_Auxin0hrs-FF1-BinC-PCR2-Rep1_S117",
"jesse-engreitz:measurement_CRUDO_FAM3C_Auxin0hrs-FF1-BinC-PCR3-Rep1_S165",
"jesse-engreitz:measurement_CRUDO_FAM3C_Auxin0hrs-FF1-BinC-PCR4-Rep1_S171"
],
"preferred_assay_title": "CRISPR FlowFISH screen"
}
],
"release_timestamp": "2024-07-10T20:10:53.347627+00:00",
"samples": [
{
"@id": "/in-vitro-systems/IGVFSM3123SZYY/",
"@type": [
"InVitroSystem",
"Biosample",
"Sample",
"Item"
],
"accession": "IGVFSM3123SZYY",
"aliases": [
"jesse-engreitz:in-vitro-system_CRUDO_FAM3C_Auxin0hrs-FF1-BinC-PCR1-Rep1_S111",
"jesse-engreitz:in-vitro-system_CRUDO_FAM3C_Auxin0hrs-FF1-BinC-PCR2-Rep1_S117",
"jesse-engreitz:in-vitro-system_CRUDO_FAM3C_Auxin0hrs-FF1-BinC-PCR3-Rep1_S165",
"jesse-engreitz:in-vitro-system_CRUDO_FAM3C_Auxin0hrs-FF1-BinC-PCR4-Rep1_S171"
],
"classifications": [
"cell line"
],
"construct_library_sets": [
"/construct-library-sets/IGVFDS1891GTLU/"
],
"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 FAM3C) 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": "2024-06-01T01:50:56.162564+00:00",
"summary": "gRNA sequencing for CRISPR interference FlowFISH screen integrating a guide (sgRNA) library targeting accessible genome regions in many genomic loci",
"uuid": "c959b707-9f45-438a-a0bb-3f617413fc32"
}