{
"@context": "/terms/",
"@id": "/measurement-sets/IGVFDS9337ZLNA/",
"@type": [
"MeasurementSet",
"FileSet",
"Item"
],
"accession": "IGVFDS9337ZLNA",
"aliases": [
"jesse-engreitz:measurement_CRUDO_SSFA2-Auxin6hrs-FF2-BinE-PCR1-Rep1_S41",
"jesse-engreitz:measurement_CRUDO_SSFA2-Auxin6hrs-FF2-BinE-PCR2-Rep1_S47",
"jesse-engreitz:measurement_CRUDO_SSFA2-Auxin6hrs-FF2-BinE-PCR3-Rep1_S95",
"jesse-engreitz:measurement_CRUDO_SSFA2-Auxin6hrs-FF2-BinE-PCR4-Rep1_S101"
],
"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": "Measurement set [IGVFDS9337ZLNA](/measurement-sets/IGVFDS9337ZLNA/) 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/IGVFDS9337ZLNA/"
},
{
"category": "missing sequencing kit",
"detail": "Measurement set [IGVFDS9337ZLNA](/measurement-sets/IGVFDS9337ZLNA/) has sequence file(s) [IGVFFI7228DOIR](/sequence-files/IGVFFI7228DOIR/), [IGVFFI1256JDZP](/sequence-files/IGVFFI1256JDZP/), [IGVFFI4668DAZM](/sequence-files/IGVFFI4668DAZM/), [IGVFFI1967IIXO](/sequence-files/IGVFFI1967IIXO/) 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/IGVFDS9337ZLNA/"
},
{
"category": "missing publication",
"detail": "In vitro system [IGVFSM1662MZZB](/in-vitro-systems/IGVFSM1662MZZB/) 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/IGVFSM1662MZZB/"
},
{
"category": "missing publication",
"detail": "Auxiliary set [IGVFDS3809LQRK](/auxiliary-sets/IGVFDS3809LQRK/) 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/IGVFDS3809LQRK/"
}
],
"WARNING": [
{
"category": "missing nucleic acid delivery",
"detail": "In vitro system [IGVFSM1662MZZB](/in-vitro-systems/IGVFSM1662MZZB/) 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/IGVFSM1662MZZB/"
}
]
},
"auxiliary_sets": [
{
"@id": "/auxiliary-sets/IGVFDS3809LQRK/",
"accession": "IGVFDS3809LQRK",
"aliases": [
"jesse-engreitz:auxiliary_sortparams_CRUDO_SSFA2-Auxin6hrs-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": "2024-05-14T20:55:12.564504+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/IGVFFI1367YZPA/",
"accession": "IGVFFI1367YZPA",
"aliases": [
"jesse-engreitz:seqspecfile_CRUDO_SSFA2-Auxin6hrs-FF2-BinE-PCR1-Rep1_S41"
],
"content_type": "seqspec",
"creation_timestamp": "2024-06-11T20:40:55.492275+00:00",
"file_format": "yaml",
"file_size": 913,
"href": "/configuration-files/IGVFFI1367YZPA/@@download/IGVFFI1367YZPA.yaml.gz",
"md5sum": "7550e5f7ed8688e078523822be40dbe0",
"s3_uri": "s3://igvf-files/2024/06/11/fdc35a23-a98d-4a6a-83a2-d33c00e30d9e/IGVFFI1367YZPA.yaml.gz",
"status": "released",
"submitted_file_name": "/oak/stanford/groups/engreitz/Projects/Cohesin/240410_IGVF_upload/seqspec/guideseq.out.SSFA2-Auxin6hrs-FF2-BinE-PCR1-Rep1_S41.yaml",
"upload_status": "validation exempted"
},
{
"@id": "/configuration-files/IGVFFI1493AADV/",
"accession": "IGVFFI1493AADV",
"aliases": [
"jesse-engreitz:seqspecfile_CRUDO_SSFA2-Auxin6hrs-FF2-BinE-PCR2-Rep1_S47"
],
"content_type": "seqspec",
"creation_timestamp": "2024-06-11T20:41:11.685764+00:00",
"file_format": "yaml",
"file_size": 913,
"href": "/configuration-files/IGVFFI1493AADV/@@download/IGVFFI1493AADV.yaml.gz",
"md5sum": "38bfe1ab5070c297c6d087fdd493ec31",
"s3_uri": "s3://igvf-files/2024/06/11/7fb563d0-77c6-4076-9f18-36a14afded3a/IGVFFI1493AADV.yaml.gz",
"status": "released",
"submitted_file_name": "/oak/stanford/groups/engreitz/Projects/Cohesin/240410_IGVF_upload/seqspec/guideseq.out.SSFA2-Auxin6hrs-FF2-BinE-PCR2-Rep1_S47.yaml",
"upload_status": "validation exempted"
},
{
"@id": "/configuration-files/IGVFFI9275HAUL/",
"accession": "IGVFFI9275HAUL",
"aliases": [
"jesse-engreitz:seqspecfile_CRUDO_SSFA2-Auxin6hrs-FF2-BinE-PCR4-Rep1_S101"
],
"content_type": "seqspec",
"creation_timestamp": "2024-06-11T20:41:42.794086+00:00",
"file_format": "yaml",
"file_size": 915,
"href": "/configuration-files/IGVFFI9275HAUL/@@download/IGVFFI9275HAUL.yaml.gz",
"md5sum": "0a88d364367d6bf396e2a3c9c06cc530",
"s3_uri": "s3://igvf-files/2024/06/11/78f3d2af-9755-43d4-a463-be570ae004c8/IGVFFI9275HAUL.yaml.gz",
"status": "released",
"submitted_file_name": "/oak/stanford/groups/engreitz/Projects/Cohesin/240410_IGVF_upload/seqspec/guideseq.out.SSFA2-Auxin6hrs-FF2-BinE-PCR4-Rep1_S101.yaml",
"upload_status": "validation exempted"
},
{
"@id": "/sequence-files/IGVFFI7228DOIR/",
"accession": "IGVFFI7228DOIR",
"aliases": [
"jesse-engreitz:auxiliary_file_CRUDO_SSFA2-Auxin6hrs-FF2-BinE-PCR3-Rep1_S95"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2024-06-01T01:49:05.184677+00:00",
"file_format": "fastq",
"file_size": 20486641,
"href": "/sequence-files/IGVFFI7228DOIR/@@download/IGVFFI7228DOIR.fastq.gz",
"md5sum": "70d15a352bb6c5308db56949f16a4431",
"s3_uri": "s3://igvf-files/2024/06/01/88671496-8d97-49dd-9ba2-1032ea972fa6/IGVFFI7228DOIR.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-Auxin6hrs-FF2-BinE-PCR3-Rep1_S95_R1_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI1256JDZP/",
"accession": "IGVFFI1256JDZP",
"aliases": [
"jesse-engreitz:auxiliary_file_CRUDO_SSFA2-Auxin6hrs-FF2-BinE-PCR1-Rep1_S41"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2024-06-01T01:48:30.148497+00:00",
"file_format": "fastq",
"file_size": 10784945,
"href": "/sequence-files/IGVFFI1256JDZP/@@download/IGVFFI1256JDZP.fastq.gz",
"md5sum": "f64f7c71013a8324016cab0a52514148",
"s3_uri": "s3://igvf-files/2024/06/01/1db04a65-b305-4e6a-badf-fe0cb5236f84/IGVFFI1256JDZP.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-Auxin6hrs-FF2-BinE-PCR1-Rep1_S41_R1_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/configuration-files/IGVFFI6763TOPA/",
"accession": "IGVFFI6763TOPA",
"aliases": [
"jesse-engreitz:seqspecfile_CRUDO_SSFA2-Auxin6hrs-FF2-BinE-PCR3-Rep1_S95"
],
"content_type": "seqspec",
"creation_timestamp": "2024-06-11T20:41:27.240815+00:00",
"file_format": "yaml",
"file_size": 912,
"href": "/configuration-files/IGVFFI6763TOPA/@@download/IGVFFI6763TOPA.yaml.gz",
"md5sum": "14816cf775905807a150a7afa5af83cb",
"s3_uri": "s3://igvf-files/2024/06/11/d656b880-b879-4f71-a8f9-a66bdbee3b85/IGVFFI6763TOPA.yaml.gz",
"status": "released",
"submitted_file_name": "/oak/stanford/groups/engreitz/Projects/Cohesin/240410_IGVF_upload/seqspec/guideseq.out.SSFA2-Auxin6hrs-FF2-BinE-PCR3-Rep1_S95.yaml",
"upload_status": "validation exempted"
},
{
"@id": "/sequence-files/IGVFFI4668DAZM/",
"accession": "IGVFFI4668DAZM",
"aliases": [
"jesse-engreitz:auxiliary_file_CRUDO_SSFA2-Auxin6hrs-FF2-BinE-PCR4-Rep1_S101"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2024-06-01T01:49:24.127826+00:00",
"file_format": "fastq",
"file_size": 2093063,
"href": "/sequence-files/IGVFFI4668DAZM/@@download/IGVFFI4668DAZM.fastq.gz",
"md5sum": "3d21777385df754ce009d43c1ed28116",
"s3_uri": "s3://igvf-files/2024/06/01/32626f42-94b0-4627-aff9-625476711673/IGVFFI4668DAZM.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-Auxin6hrs-FF2-BinE-PCR4-Rep1_S101_R1_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI1967IIXO/",
"accession": "IGVFFI1967IIXO",
"aliases": [
"jesse-engreitz:auxiliary_file_CRUDO_SSFA2-Auxin6hrs-FF2-BinE-PCR2-Rep1_S47"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2024-06-01T01:48:47.770983+00:00",
"file_format": "fastq",
"file_size": 2191720,
"href": "/sequence-files/IGVFFI1967IIXO/@@download/IGVFFI1967IIXO.fastq.gz",
"md5sum": "a768b122c69d487806a8ecc578750521",
"s3_uri": "s3://igvf-files/2024/06/01/9f5b2c0f-2022-4ea0-8056-acf819ce90a3/IGVFFI1967IIXO.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-Auxin6hrs-FF2-BinE-PCR2-Rep1_S47_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": "2024-07-10T19:53:09.109657+00:00",
"samples": [
{
"@id": "/in-vitro-systems/IGVFSM1662MZZB/",
"@type": [
"InVitroSystem",
"Biosample",
"Sample",
"Item"
],
"accession": "IGVFSM1662MZZB",
"aliases": [
"jesse-engreitz:in-vitro-system_CRUDO_SSFA2-Auxin6hrs-FF2-BinE-PCR1-Rep1_S41",
"jesse-engreitz:in-vitro-system_CRUDO_SSFA2-Auxin6hrs-FF2-BinE-PCR2-Rep1_S47",
"jesse-engreitz:in-vitro-system_CRUDO_SSFA2-Auxin6hrs-FF2-BinE-PCR3-Rep1_S95",
"jesse-engreitz:in-vitro-system_CRUDO_SSFA2-Auxin6hrs-FF2-BinE-PCR4-Rep1_S101"
],
"classifications": [
"cell line"
],
"institutional_certificates": [],
"modifications": [
{
"@id": "/degron-modifications/95081d1b-08b4-49ed-b324-e53fc43d8456/",
"modality": "degradation",
"status": "released"
},
{
"@id": "/crispr-modifications/8543fa06-1720-4e7d-8e8f-7e24c1b1cf79/",
"modality": "interference",
"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 E for 80-90% expression of SSFA2) treated with 1 μM 5-Phenyl-1H-indole-3-acetic acid for 6 hours, modified with AID system targeting RAD21, CRISPRi Sp-dCas9-KOX1-KRAB, transfected with a guide library",
"taxa": "Homo sapiens",
"treatments": [
{
"@id": "/treatments/d35868d1-c45b-49ae-8ff3-a9c0c22551c2/",
"purpose": "activation",
"status": "released",
"summary": "Treatment of 1 μM 5-Phenyl-1H-indole-3-acetic acid for 6 hours",
"treatment_term_name": "5-Phenyl-1H-indole-3-acetic acid",
"treatment_type": "chemical"
}
]
}
],
"schema_version": "26",
"status": "released",
"submitted_by": {
"@id": "/users/3bd6f74c-8cf3-4c35-a94d-0c7c11654815/",
"title": "Chongyon Park"
},
"submitted_files_timestamp": "2024-06-01T01:48:30.148497+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": "5c7a84dc-8630-4bb8-8de6-99fefbaf85e5"
}