{
"@context": "/terms/",
"@id": "/measurement-sets/IGVFDS6103MEVT/",
"@type": [
"MeasurementSet",
"FileSet",
"Item"
],
"accession": "IGVFDS6103MEVT",
"aliases": [
"jesse-engreitz:measurement_CRUDO_SSFA2-Auxin0hrs-FF2-BinC-PCR1-Rep1_S15",
"jesse-engreitz:measurement_CRUDO_SSFA2-Auxin0hrs-FF2-BinC-PCR2-Rep1_S21",
"jesse-engreitz:measurement_CRUDO_SSFA2-Auxin0hrs-FF2-BinC-PCR3-Rep1_S69",
"jesse-engreitz:measurement_CRUDO_SSFA2-Auxin0hrs-FF2-BinC-PCR4-Rep1_S75"
],
"assay_term": {
"@id": "/assay-terms/OBI_0003661/",
"assay_slims": [
"CRISPR screens"
],
"status": "released",
"term_name": "in vitro CRISPR screen using flow cytometry"
},
"audit": {
"INTERNAL_ACTION": [
{
"category": "missing publication",
"detail": "Auxiliary set [IGVFDS4597CMXX](/auxiliary-sets/IGVFDS4597CMXX/) has no `publications`. Released and archived file sets are expected to be associated with a publication.",
"level": 30,
"level_name": "INTERNAL_ACTION",
"name": "audit_file_set_missing_publication",
"path": "/auxiliary-sets/IGVFDS4597CMXX/"
},
{
"category": "missing publication",
"detail": "In vitro system [IGVFSM8438GPDC](/in-vitro-systems/IGVFSM8438GPDC/) has no `publications`. Released and archived samples are expected to be associated with a publication.",
"level": 30,
"level_name": "INTERNAL_ACTION",
"name": "audit_sample_missing_publication",
"path": "/in-vitro-systems/IGVFSM8438GPDC/"
},
{
"category": "missing publication",
"detail": "Measurement set [IGVFDS6103MEVT](/measurement-sets/IGVFDS6103MEVT/) has no `publications`. Released and archived file sets are expected to be associated with a publication.",
"level": 30,
"level_name": "INTERNAL_ACTION",
"name": "audit_file_set_missing_publication",
"path": "/measurement-sets/IGVFDS6103MEVT/"
},
{
"category": "missing sequencing kit",
"detail": "Measurement set [IGVFDS6103MEVT](/measurement-sets/IGVFDS6103MEVT/) has sequence file(s) [IGVFFI3952UPLD](/sequence-files/IGVFFI3952UPLD/), [IGVFFI5250HUCB](/sequence-files/IGVFFI5250HUCB/), [IGVFFI8622TDNM](/sequence-files/IGVFFI8622TDNM/), [IGVFFI3227NNAQ](/sequence-files/IGVFFI3227NNAQ/) which lack specification of a `sequencing_kit`. Sequence files in a file set associated wtih bulk data should specify a sequencing kit.",
"level": 30,
"level_name": "INTERNAL_ACTION",
"name": "audit_inconsistent_sequencing_kit",
"path": "/measurement-sets/IGVFDS6103MEVT/"
}
],
"WARNING": [
{
"category": "missing nucleic acid delivery",
"detail": "In vitro system [IGVFSM8438GPDC](/in-vitro-systems/IGVFSM8438GPDC/) has `construct_library_sets` but is missing `nucleic_acid_delivery`. Samples linked to construct library sets are expected to specify nucleic acid delivery method.",
"level": 40,
"level_name": "WARNING",
"name": "audit_missing_nucleic_acid_delivery",
"path": "/in-vitro-systems/IGVFSM8438GPDC/"
}
]
},
"auxiliary_sets": [
{
"@id": "/auxiliary-sets/IGVFDS4597CMXX/",
"accession": "IGVFDS4597CMXX",
"aliases": [
"jesse-engreitz:auxiliary_sortparams_CRUDO_SSFA2-Auxin0hrs-FF2"
],
"file_set_type": "cell sorting",
"status": "released"
}
],
"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"
},
"construct_library_sets": [
{
"@id": "/construct-library-sets/IGVFDS5413RKIA/",
"accession": "IGVFDS5413RKIA",
"file_set_type": "guide library",
"integrated_content_files": [
{
"@id": "/tabular-files/IGVFFI5130EWUZ/",
"accession": "IGVFFI5130EWUZ",
"content_type": "guide RNA sequences",
"status": "released",
"summary": "guide RNA sequences"
}
],
"status": "released",
"summary": "guide (sgRNA) library targeting accessible genome regions in many genomic loci"
}
],
"control_for": [],
"creation_timestamp": "2024-05-14T20:33:15.370409+00:00",
"data_use_limitation_summaries": [
"no certificate"
],
"documents": [
"/documents/74d53b9c-ab1d-42e3-b679-d3a00ae3d842/"
],
"donors": [
{
"@id": "/human-donors/IGVFDO0384OZRW/",
"accession": "IGVFDO0384OZRW",
"aliases": [
"igvf:donor_of_HCT116"
],
"sex": "male",
"status": "released",
"taxa": "Homo sapiens"
}
],
"externally_hosted": false,
"file_set_type": "experimental data",
"files": [
{
"@id": "/configuration-files/IGVFFI7304ZIDV/",
"accession": "IGVFFI7304ZIDV",
"aliases": [
"jesse-engreitz:seqspecfile_CRUDO_SSFA2-Auxin0hrs-FF2-BinC-PCR1-Rep1_S15"
],
"content_type": "seqspec",
"creation_timestamp": "2024-06-11T20:38:22.733909+00:00",
"file_format": "yaml",
"file_size": 913,
"href": "/configuration-files/IGVFFI7304ZIDV/@@download/IGVFFI7304ZIDV.yaml.gz",
"md5sum": "e6ddee37cfba4f31018ce3e59d98be14",
"s3_uri": "s3://igvf-files/2024/06/11/45dafe10-cc14-47ba-be08-9df070501866/IGVFFI7304ZIDV.yaml.gz",
"status": "released",
"submitted_file_name": "/oak/stanford/groups/engreitz/Projects/Cohesin/240410_IGVF_upload/seqspec/guideseq.out.SSFA2-Auxin0hrs-FF2-BinC-PCR1-Rep1_S15.yaml",
"upload_status": "validation exempted"
},
{
"@id": "/configuration-files/IGVFFI9956XLRB/",
"accession": "IGVFFI9956XLRB",
"aliases": [
"jesse-engreitz:seqspecfile_CRUDO_SSFA2-Auxin0hrs-FF2-BinC-PCR2-Rep1_S21"
],
"content_type": "seqspec",
"creation_timestamp": "2024-06-11T20:38:38.329827+00:00",
"file_format": "yaml",
"file_size": 912,
"href": "/configuration-files/IGVFFI9956XLRB/@@download/IGVFFI9956XLRB.yaml.gz",
"md5sum": "2bd127fecd3b9c5fe70086092bca9d28",
"s3_uri": "s3://igvf-files/2024/06/11/a49fe185-b57b-479b-ac0e-20c207debad4/IGVFFI9956XLRB.yaml.gz",
"status": "released",
"submitted_file_name": "/oak/stanford/groups/engreitz/Projects/Cohesin/240410_IGVF_upload/seqspec/guideseq.out.SSFA2-Auxin0hrs-FF2-BinC-PCR2-Rep1_S21.yaml",
"upload_status": "validation exempted"
},
{
"@id": "/configuration-files/IGVFFI2564WQBV/",
"accession": "IGVFFI2564WQBV",
"aliases": [
"jesse-engreitz:seqspecfile_CRUDO_SSFA2-Auxin0hrs-FF2-BinC-PCR3-Rep1_S69"
],
"content_type": "seqspec",
"creation_timestamp": "2024-06-11T20:39:16.887824+00:00",
"file_format": "yaml",
"file_size": 912,
"href": "/configuration-files/IGVFFI2564WQBV/@@download/IGVFFI2564WQBV.yaml.gz",
"md5sum": "cb2aed9da84f80bd62598920816c1a27",
"s3_uri": "s3://igvf-files/2024/06/11/ac60fe2b-9bef-492f-999f-ceeb4e6e4828/IGVFFI2564WQBV.yaml.gz",
"status": "released",
"submitted_file_name": "/oak/stanford/groups/engreitz/Projects/Cohesin/240410_IGVF_upload/seqspec/guideseq.out.SSFA2-Auxin0hrs-FF2-BinC-PCR3-Rep1_S69.yaml",
"upload_status": "validation exempted"
},
{
"@id": "/configuration-files/IGVFFI2975BGQX/",
"accession": "IGVFFI2975BGQX",
"aliases": [
"jesse-engreitz:seqspecfile_CRUDO_SSFA2-Auxin0hrs-FF2-BinC-PCR4-Rep1_S75"
],
"content_type": "seqspec",
"creation_timestamp": "2024-06-11T20:39:32.374733+00:00",
"file_format": "yaml",
"file_size": 913,
"href": "/configuration-files/IGVFFI2975BGQX/@@download/IGVFFI2975BGQX.yaml.gz",
"md5sum": "a4cd7751afa60f05b07e34f79e66b132",
"s3_uri": "s3://igvf-files/2024/06/11/ee30c74a-1e96-4a58-a8ed-4c66c2be8ca8/IGVFFI2975BGQX.yaml.gz",
"status": "released",
"submitted_file_name": "/oak/stanford/groups/engreitz/Projects/Cohesin/240410_IGVF_upload/seqspec/guideseq.out.SSFA2-Auxin0hrs-FF2-BinC-PCR4-Rep1_S75.yaml",
"upload_status": "validation exempted"
},
{
"@id": "/sequence-files/IGVFFI3952UPLD/",
"accession": "IGVFFI3952UPLD",
"aliases": [
"jesse-engreitz:auxiliary_file_CRUDO_SSFA2-Auxin0hrs-FF2-BinC-PCR1-Rep1_S15"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2024-06-01T01:45:53.847312+00:00",
"file_format": "fastq",
"file_size": 10849000,
"href": "/sequence-files/IGVFFI3952UPLD/@@download/IGVFFI3952UPLD.fastq.gz",
"md5sum": "1990d5ddf43a2e146a1665ecb3ee4c6c",
"s3_uri": "s3://igvf-files/2024/06/01/dbad0f22-1fd8-4b58-b661-6ffecce5e1de/IGVFFI3952UPLD.fastq.gz",
"sequencing_platform": {
"@id": "/platform-terms/EFO_0008565/",
"status": "released",
"term_name": "Illumina HiSeq 2500"
},
"status": "released",
"submitted_file_name": "/oak/stanford/groups/engreitz/Projects/Cohesin/220308B014_CCND1_SSFA2_FAM3C/fastq_trim/SSFA2-Auxin0hrs-FF2-BinC-PCR1-Rep1_S15_R1_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI5250HUCB/",
"accession": "IGVFFI5250HUCB",
"aliases": [
"jesse-engreitz:auxiliary_file_CRUDO_SSFA2-Auxin0hrs-FF2-BinC-PCR2-Rep1_S21"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2024-06-01T01:46:15.727706+00:00",
"file_format": "fastq",
"file_size": 15820281,
"href": "/sequence-files/IGVFFI5250HUCB/@@download/IGVFFI5250HUCB.fastq.gz",
"md5sum": "ac661d1dc7476924ad1a810276fa1494",
"s3_uri": "s3://igvf-files/2024/06/01/2f41b100-9878-4c19-9a4d-eec07d690cb1/IGVFFI5250HUCB.fastq.gz",
"sequencing_platform": {
"@id": "/platform-terms/EFO_0008565/",
"status": "released",
"term_name": "Illumina HiSeq 2500"
},
"status": "released",
"submitted_file_name": "/oak/stanford/groups/engreitz/Projects/Cohesin/220308B014_CCND1_SSFA2_FAM3C/fastq_trim/SSFA2-Auxin0hrs-FF2-BinC-PCR2-Rep1_S21_R1_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI8622TDNM/",
"accession": "IGVFFI8622TDNM",
"aliases": [
"jesse-engreitz:auxiliary_file_CRUDO_SSFA2-Auxin0hrs-FF2-BinC-PCR4-Rep1_S75"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2024-06-01T01:46:52.829493+00:00",
"file_format": "fastq",
"file_size": 18707865,
"href": "/sequence-files/IGVFFI8622TDNM/@@download/IGVFFI8622TDNM.fastq.gz",
"md5sum": "a85d5647667ddb32abaed42b53d5eb69",
"s3_uri": "s3://igvf-files/2024/06/01/f7e7249d-8f13-4cd1-80b6-6a173dc1cdf8/IGVFFI8622TDNM.fastq.gz",
"sequencing_platform": {
"@id": "/platform-terms/EFO_0008565/",
"status": "released",
"term_name": "Illumina HiSeq 2500"
},
"status": "released",
"submitted_file_name": "/oak/stanford/groups/engreitz/Projects/Cohesin/220308B014_CCND1_SSFA2_FAM3C/fastq_trim/SSFA2-Auxin0hrs-FF2-BinC-PCR4-Rep1_S75_R1_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI3227NNAQ/",
"accession": "IGVFFI3227NNAQ",
"aliases": [
"jesse-engreitz:auxiliary_file_CRUDO_SSFA2-Auxin0hrs-FF2-BinC-PCR3-Rep1_S69"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2024-06-01T01:46:34.986333+00:00",
"file_format": "fastq",
"file_size": 20511350,
"href": "/sequence-files/IGVFFI3227NNAQ/@@download/IGVFFI3227NNAQ.fastq.gz",
"md5sum": "9a1e4d81953cfb6aebf89da73f34be65",
"s3_uri": "s3://igvf-files/2024/06/01/8037516d-443c-4325-a655-3ce9d33cbfee/IGVFFI3227NNAQ.fastq.gz",
"sequencing_platform": {
"@id": "/platform-terms/EFO_0008565/",
"status": "released",
"term_name": "Illumina HiSeq 2500"
},
"status": "released",
"submitted_file_name": "/oak/stanford/groups/engreitz/Projects/Cohesin/220308B014_CCND1_SSFA2_FAM3C/fastq_trim/SSFA2-Auxin0hrs-FF2-BinC-PCR3-Rep1_S69_R1_001.fastq.gz",
"upload_status": "validated"
}
],
"input_for": [
"/analysis-sets/IGVFDS2031CTSP/"
],
"lab": {
"@id": "/labs/jesse-engreitz/",
"title": "Jesse Engreitz, Stanford"
},
"notes": "The readout 2e41e624-f6c7-4f0c-a07e-bc36cefdca39 was removed from this measurement set.",
"preferred_assay_title": "CRISPR FlowFISH screen",
"protocols": [
"https://www.protocols.io/view/crispri-of-regulatory-elements-upon-degron-operati-5jyl82d59l2w/v1"
],
"release_timestamp": "2024-07-10T19:51:38.420931+00:00",
"samples": [
{
"@id": "/in-vitro-systems/IGVFSM8438GPDC/",
"@type": [
"InVitroSystem",
"Biosample",
"Sample",
"Item"
],
"accession": "IGVFSM8438GPDC",
"aliases": [
"jesse-engreitz:in-vitro-system_CRUDO_SSFA2-Auxin0hrs-FF2-BinC-PCR1-Rep1_S15",
"jesse-engreitz:in-vitro-system_CRUDO_SSFA2-Auxin0hrs-FF2-BinC-PCR2-Rep1_S21",
"jesse-engreitz:in-vitro-system_CRUDO_SSFA2-Auxin0hrs-FF2-BinC-PCR3-Rep1_S69",
"jesse-engreitz:in-vitro-system_CRUDO_SSFA2-Auxin0hrs-FF2-BinC-PCR4-Rep1_S75"
],
"classifications": [
"cell line"
],
"institutional_certificates": [],
"modifications": [
{
"@id": "/crispr-modifications/8543fa06-1720-4e7d-8e8f-7e24c1b1cf79/",
"modality": "interference",
"status": "released"
},
{
"@id": "/degron-modifications/2e8d10cc-fc98-44d5-a7d9-e2892e16c98a/",
"modality": "degradation",
"status": "released"
}
],
"sample_terms": [
{
"@id": "/sample-terms/EFO_0002824/",
"@type": [
"SampleTerm",
"OntologyTerm",
"Item"
],
"aliases": [
"igvf:HCT116"
],
"status": "released",
"summary": "HCT116",
"term_name": "HCT116"
}
],
"status": "released",
"summary": "Homo sapiens (male) HCT116 cell line (sorting details: FACS bin C for 35-45% expression of SSFA2) modified with CRISPRi Sp-dCas9-KOX1-KRAB, inactive AID system targeting RAD21, transfected with a guide library",
"taxa": "Homo sapiens"
}
],
"schema_version": "26",
"status": "released",
"submitted_by": {
"@id": "/users/3bd6f74c-8cf3-4c35-a94d-0c7c11654815/",
"title": "Chongyon Park"
},
"submitted_files_timestamp": "2024-06-01T01:45:53.847312+00:00",
"summary": "mixed CRISPR FlowFISH screen sorted on the expression of ITPRID2 integrating a guide (sgRNA) library targeting accessible genome regions in many genomic loci",
"targeted_genes": [
{
"@id": "/genes/ENSG00000138434/",
"geneid": "ENSG00000138434",
"name": "ITPR interacting domain containing 2",
"status": "released",
"symbol": "ITPRID2",
"synonyms": [
"sperm associated antigen 13",
"ITPR interacting domain containing 2",
"ITPR-interacting domain-containing protein 2",
"SSFA2",
"KRAS-induced actin-interacting protein",
"cleavage signal-1 protein",
"ki-ras-induced actin-interacting protein",
"sperm specific antigen 2",
"ITPRID2",
"SPAG13",
"protein ITPRID2",
"CS-1",
"CS1",
"KRAP"
]
}
],
"uuid": "68c8f339-c15a-42f6-952c-d61900757e46"
}