{
"@context": "/terms/",
"@id": "/measurement-sets/IGVFDS8098OGBN/",
"@type": [
"MeasurementSet",
"FileSet",
"Item"
],
"accession": "IGVFDS8098OGBN",
"aliases": [
"jesse-engreitz:measurement_CRUDO_SSFA2-Auxin0hrs-FF2-BinE-PCR1-Rep1_S17",
"jesse-engreitz:measurement_CRUDO_SSFA2-Auxin0hrs-FF2-BinE-PCR2-Rep1_S23",
"jesse-engreitz:measurement_CRUDO_SSFA2-Auxin0hrs-FF2-BinE-PCR3-Rep1_S71",
"jesse-engreitz:measurement_CRUDO_SSFA2-Auxin0hrs-FF2-BinE-PCR4-Rep1_S77"
],
"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 [IGVFDS8098OGBN](/measurement-sets/IGVFDS8098OGBN/) 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/IGVFDS8098OGBN/"
},
{
"category": "missing sequencing kit",
"detail": "Measurement set [IGVFDS8098OGBN](/measurement-sets/IGVFDS8098OGBN/) has sequence file(s) [IGVFFI7752CYYJ](/sequence-files/IGVFFI7752CYYJ/), [IGVFFI6094QETO](/sequence-files/IGVFFI6094QETO/), [IGVFFI8646GHGN](/sequence-files/IGVFFI8646GHGN/), [IGVFFI4315EDNJ](/sequence-files/IGVFFI4315EDNJ/) 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/IGVFDS8098OGBN/"
},
{
"category": "missing publication",
"detail": "In vitro system [IGVFSM9097DRIA](/in-vitro-systems/IGVFSM9097DRIA/) 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/IGVFSM9097DRIA/"
},
{
"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/"
}
],
"WARNING": [
{
"category": "missing nucleic acid delivery",
"detail": "In vitro system [IGVFSM9097DRIA](/in-vitro-systems/IGVFSM9097DRIA/) 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/IGVFSM9097DRIA/"
}
]
},
"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": "2024-05-14T20:33:17.098591+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/IGVFFI5168BJYX/",
"accession": "IGVFFI5168BJYX",
"aliases": [
"jesse-engreitz:seqspecfile_CRUDO_SSFA2-Auxin0hrs-FF2-BinE-PCR2-Rep1_S23"
],
"content_type": "seqspec",
"creation_timestamp": "2024-06-11T20:38:43.507832+00:00",
"file_format": "yaml",
"file_size": 913,
"href": "/configuration-files/IGVFFI5168BJYX/@@download/IGVFFI5168BJYX.yaml.gz",
"md5sum": "6639bd4c33682fbd10283cb9e0e393f8",
"s3_uri": "s3://igvf-files/2024/06/11/ed0867b0-4f40-443f-8095-2a179f68bd71/IGVFFI5168BJYX.yaml.gz",
"status": "released",
"submitted_file_name": "/oak/stanford/groups/engreitz/Projects/Cohesin/240410_IGVF_upload/seqspec/guideseq.out.SSFA2-Auxin0hrs-FF2-BinE-PCR2-Rep1_S23.yaml",
"upload_status": "validation exempted"
},
{
"@id": "/configuration-files/IGVFFI3316VTMT/",
"accession": "IGVFFI3316VTMT",
"aliases": [
"jesse-engreitz:seqspecfile_CRUDO_SSFA2-Auxin0hrs-FF2-BinE-PCR1-Rep1_S17"
],
"content_type": "seqspec",
"creation_timestamp": "2024-06-11T20:38:28.029318+00:00",
"file_format": "yaml",
"file_size": 913,
"href": "/configuration-files/IGVFFI3316VTMT/@@download/IGVFFI3316VTMT.yaml.gz",
"md5sum": "259958e91d8e8b3fde11449230dd7448",
"s3_uri": "s3://igvf-files/2024/06/11/85fd1a9d-04d6-4a83-9ae4-9dbe29db0e20/IGVFFI3316VTMT.yaml.gz",
"status": "released",
"submitted_file_name": "/oak/stanford/groups/engreitz/Projects/Cohesin/240410_IGVF_upload/seqspec/guideseq.out.SSFA2-Auxin0hrs-FF2-BinE-PCR1-Rep1_S17.yaml",
"upload_status": "validation exempted"
},
{
"@id": "/configuration-files/IGVFFI4784OLOD/",
"accession": "IGVFFI4784OLOD",
"aliases": [
"jesse-engreitz:seqspecfile_CRUDO_SSFA2-Auxin0hrs-FF2-BinE-PCR3-Rep1_S71"
],
"content_type": "seqspec",
"creation_timestamp": "2024-06-11T20:39:22.214545+00:00",
"file_format": "yaml",
"file_size": 912,
"href": "/configuration-files/IGVFFI4784OLOD/@@download/IGVFFI4784OLOD.yaml.gz",
"md5sum": "a2c80d45a6ed3b30719551989c7badba",
"s3_uri": "s3://igvf-files/2024/06/11/43cbe569-08db-4c7f-9ebb-95d2a903aa3d/IGVFFI4784OLOD.yaml.gz",
"status": "released",
"submitted_file_name": "/oak/stanford/groups/engreitz/Projects/Cohesin/240410_IGVF_upload/seqspec/guideseq.out.SSFA2-Auxin0hrs-FF2-BinE-PCR3-Rep1_S71.yaml",
"upload_status": "validation exempted"
},
{
"@id": "/configuration-files/IGVFFI0392HWSG/",
"accession": "IGVFFI0392HWSG",
"aliases": [
"jesse-engreitz:seqspecfile_CRUDO_SSFA2-Auxin0hrs-FF2-BinE-PCR4-Rep1_S77"
],
"content_type": "seqspec",
"creation_timestamp": "2024-06-11T20:39:38.091137+00:00",
"file_format": "yaml",
"file_size": 911,
"href": "/configuration-files/IGVFFI0392HWSG/@@download/IGVFFI0392HWSG.yaml.gz",
"md5sum": "d3af1ed43e7b263ae86479bc585270cf",
"s3_uri": "s3://igvf-files/2024/06/11/cf53b9cb-581f-4582-bbea-090e206a46b2/IGVFFI0392HWSG.yaml.gz",
"status": "released",
"submitted_file_name": "/oak/stanford/groups/engreitz/Projects/Cohesin/240410_IGVF_upload/seqspec/guideseq.out.SSFA2-Auxin0hrs-FF2-BinE-PCR4-Rep1_S77.yaml",
"upload_status": "validation exempted"
},
{
"@id": "/sequence-files/IGVFFI7752CYYJ/",
"accession": "IGVFFI7752CYYJ",
"aliases": [
"jesse-engreitz:auxiliary_file_CRUDO_SSFA2-Auxin0hrs-FF2-BinE-PCR1-Rep1_S17"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2024-06-01T01:46:03.633426+00:00",
"file_format": "fastq",
"file_size": 9130239,
"href": "/sequence-files/IGVFFI7752CYYJ/@@download/IGVFFI7752CYYJ.fastq.gz",
"md5sum": "63cc942ae730fccd0c1dcfedc95bf451",
"s3_uri": "s3://igvf-files/2024/06/01/f1725405-7e26-42d5-b449-13f52bea58cf/IGVFFI7752CYYJ.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-BinE-PCR1-Rep1_S17_R1_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI6094QETO/",
"accession": "IGVFFI6094QETO",
"aliases": [
"jesse-engreitz:auxiliary_file_CRUDO_SSFA2-Auxin0hrs-FF2-BinE-PCR3-Rep1_S71"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2024-06-01T01:46:40.966016+00:00",
"file_format": "fastq",
"file_size": 14344858,
"href": "/sequence-files/IGVFFI6094QETO/@@download/IGVFFI6094QETO.fastq.gz",
"md5sum": "eee3a75bb62b659b0cd873f9ecc4d7ae",
"s3_uri": "s3://igvf-files/2024/06/01/3e20f801-835d-4a18-9032-209ef76b7075/IGVFFI6094QETO.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-BinE-PCR3-Rep1_S71_R1_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI8646GHGN/",
"accession": "IGVFFI8646GHGN",
"aliases": [
"jesse-engreitz:auxiliary_file_CRUDO_SSFA2-Auxin0hrs-FF2-BinE-PCR4-Rep1_S77"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2024-06-01T01:46:58.883877+00:00",
"file_format": "fastq",
"file_size": 20050660,
"href": "/sequence-files/IGVFFI8646GHGN/@@download/IGVFFI8646GHGN.fastq.gz",
"md5sum": "b1bdf3cffc8aa2fa7b22e70be995ba32",
"s3_uri": "s3://igvf-files/2024/06/01/5523ffb8-5160-446b-963a-418279843f0b/IGVFFI8646GHGN.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-BinE-PCR4-Rep1_S77_R1_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI4315EDNJ/",
"accession": "IGVFFI4315EDNJ",
"aliases": [
"jesse-engreitz:auxiliary_file_CRUDO_SSFA2-Auxin0hrs-FF2-BinE-PCR2-Rep1_S23"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2024-06-01T01:46:23.222743+00:00",
"file_format": "fastq",
"file_size": 19460589,
"href": "/sequence-files/IGVFFI4315EDNJ/@@download/IGVFFI4315EDNJ.fastq.gz",
"md5sum": "f373c0237e3042e29b47bb9bce2ce885",
"s3_uri": "s3://igvf-files/2024/06/01/3c140bbf-4f16-40be-be23-b5e996d0cbda/IGVFFI4315EDNJ.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-BinE-PCR2-Rep1_S23_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": "2024-07-10T19:51:51.960296+00:00",
"samples": [
{
"@id": "/in-vitro-systems/IGVFSM9097DRIA/",
"@type": [
"InVitroSystem",
"Biosample",
"Sample",
"Item"
],
"accession": "IGVFSM9097DRIA",
"aliases": [
"jesse-engreitz:in-vitro-system_CRUDO_SSFA2-Auxin0hrs-FF2-BinE-PCR1-Rep1_S17",
"jesse-engreitz:in-vitro-system_CRUDO_SSFA2-Auxin0hrs-FF2-BinE-PCR2-Rep1_S23",
"jesse-engreitz:in-vitro-system_CRUDO_SSFA2-Auxin0hrs-FF2-BinE-PCR3-Rep1_S71",
"jesse-engreitz:in-vitro-system_CRUDO_SSFA2-Auxin0hrs-FF2-BinE-PCR4-Rep1_S77"
],
"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 E for 80-90% 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": "2024-06-01T01:46:03.633426+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": "edf0de8d-daea-4a7d-a46b-cb2910cf9f8d"
}