{
"@context": "/terms/",
"@id": "/measurement-sets/IGVFDS2368HJNA/",
"@type": [
"MeasurementSet",
"FileSet",
"Item"
],
"accession": "IGVFDS2368HJNA",
"aliases": [
"jesse-engreitz:measurement_CRUDO_CCND1_Auxin6hrs-FF1-BinE-PCR1-Rep1_S245",
"jesse-engreitz:measurement_CRUDO_CCND1_Auxin6hrs-FF1-BinE-PCR2-Rep1_S251",
"jesse-engreitz:measurement_CRUDO_CCND1_Auxin6hrs-FF1-BinE-PCR3-Rep1_S287",
"jesse-engreitz:measurement_CRUDO_CCND1_Auxin6hrs-FF1-BinE-PCR4-Rep1_S293"
],
"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 [IGVFDS2368HJNA](/measurement-sets/IGVFDS2368HJNA/) 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/IGVFDS2368HJNA/"
},
{
"category": "missing sequencing kit",
"detail": "Measurement set [IGVFDS2368HJNA](/measurement-sets/IGVFDS2368HJNA/) has sequence file(s) [IGVFFI0996XOGX](/sequence-files/IGVFFI0996XOGX/), [IGVFFI4198FZCC](/sequence-files/IGVFFI4198FZCC/), [IGVFFI5619AUER](/sequence-files/IGVFFI5619AUER/), [IGVFFI5866ZGPN](/sequence-files/IGVFFI5866ZGPN/) 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/IGVFDS2368HJNA/"
},
{
"category": "missing publication",
"detail": "Auxiliary set [IGVFDS6842FAIJ](/auxiliary-sets/IGVFDS6842FAIJ/) 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/IGVFDS6842FAIJ/"
},
{
"category": "missing publication",
"detail": "In vitro system [IGVFSM3721QHDS](/in-vitro-systems/IGVFSM3721QHDS/) 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/IGVFSM3721QHDS/"
}
],
"WARNING": [
{
"category": "missing nucleic acid delivery",
"detail": "In vitro system [IGVFSM3721QHDS](/in-vitro-systems/IGVFSM3721QHDS/) 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/IGVFSM3721QHDS/"
}
]
},
"auxiliary_sets": [
{
"@id": "/auxiliary-sets/IGVFDS6842FAIJ/",
"accession": "IGVFDS6842FAIJ",
"aliases": [
"jesse-engreitz:auxiliary_sortparams_CRUDO_CCND1_Auxin6hrs-FF1"
],
"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/IGVFDS6351FGNG/",
"accession": "IGVFDS6351FGNG",
"file_set_type": "guide library",
"integrated_content_files": [
{
"@id": "/tabular-files/IGVFFI5924HOIN/",
"accession": "IGVFFI5924HOIN",
"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": "2024-05-13T22:16:38.948848+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/IGVFFI4801IXZV/",
"accession": "IGVFFI4801IXZV",
"aliases": [
"jesse-engreitz:seqspecfile_CRUDO_CCND1_Auxin6hrs-FF1-BinE-PCR1-Rep1_S245"
],
"content_type": "seqspec",
"creation_timestamp": "2024-06-11T20:30:01.506095+00:00",
"file_format": "yaml",
"file_size": 914,
"href": "/configuration-files/IGVFFI4801IXZV/@@download/IGVFFI4801IXZV.yaml.gz",
"md5sum": "0bcd9ae591889035ff402bcfaf559447",
"s3_uri": "s3://igvf-files/2024/06/11/24b933e6-c98b-44b8-be78-9394f6f6d788/IGVFFI4801IXZV.yaml.gz",
"status": "released",
"submitted_file_name": "/oak/stanford/groups/engreitz/Projects/Cohesin/240410_IGVF_upload/seqspec/guideseq.out.CCND1_Auxin6hrs-FF1-BinE-PCR1-Rep1_S245.yaml",
"upload_status": "validation exempted"
},
{
"@id": "/sequence-files/IGVFFI0996XOGX/",
"accession": "IGVFFI0996XOGX",
"aliases": [
"jesse-engreitz:auxiliary_file_CRUDO_CCND1_Auxin6hrs-FF1-BinE-PCR1-Rep1_S245"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2024-06-01T01:42:12.473543+00:00",
"file_format": "fastq",
"file_size": 15063113,
"href": "/sequence-files/IGVFFI0996XOGX/@@download/IGVFFI0996XOGX.fastq.gz",
"md5sum": "6d82de74519ed7a35b7ddb8c091030e0",
"s3_uri": "s3://igvf-files/2024/06/01/e86ccab8-6f69-4988-943c-1b657b3ef908/IGVFFI0996XOGX.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/CCND1-Auxin6hrs-FF1-BinE-PCR1-Rep1_S245_R1_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/configuration-files/IGVFFI4206WEWP/",
"accession": "IGVFFI4206WEWP",
"aliases": [
"jesse-engreitz:seqspecfile_CRUDO_CCND1_Auxin6hrs-FF1-BinE-PCR2-Rep1_S251"
],
"content_type": "seqspec",
"creation_timestamp": "2024-06-11T20:30:15.655945+00:00",
"file_format": "yaml",
"file_size": 913,
"href": "/configuration-files/IGVFFI4206WEWP/@@download/IGVFFI4206WEWP.yaml.gz",
"md5sum": "c7a9da690f5739c5e7cf7b323fb26ea6",
"s3_uri": "s3://igvf-files/2024/06/11/f878d2ac-d0c5-430e-b663-7fe52af847f3/IGVFFI4206WEWP.yaml.gz",
"status": "released",
"submitted_file_name": "/oak/stanford/groups/engreitz/Projects/Cohesin/240410_IGVF_upload/seqspec/guideseq.out.CCND1_Auxin6hrs-FF1-BinE-PCR2-Rep1_S251.yaml",
"upload_status": "validation exempted"
},
{
"@id": "/configuration-files/IGVFFI9366NHKY/",
"accession": "IGVFFI9366NHKY",
"aliases": [
"jesse-engreitz:seqspecfile_CRUDO_CCND1_Auxin6hrs-FF1-BinE-PCR3-Rep1_S287"
],
"content_type": "seqspec",
"creation_timestamp": "2024-06-11T20:30:29.677954+00:00",
"file_format": "yaml",
"file_size": 913,
"href": "/configuration-files/IGVFFI9366NHKY/@@download/IGVFFI9366NHKY.yaml.gz",
"md5sum": "bd4538711069b34355a3cf55655b97f8",
"s3_uri": "s3://igvf-files/2024/06/11/71ee6ac3-ae7c-492e-b60c-98c1fbd4ca57/IGVFFI9366NHKY.yaml.gz",
"status": "released",
"submitted_file_name": "/oak/stanford/groups/engreitz/Projects/Cohesin/240410_IGVF_upload/seqspec/guideseq.out.CCND1_Auxin6hrs-FF1-BinE-PCR3-Rep1_S287.yaml",
"upload_status": "validation exempted"
},
{
"@id": "/sequence-files/IGVFFI4198FZCC/",
"accession": "IGVFFI4198FZCC",
"aliases": [
"jesse-engreitz:auxiliary_file_CRUDO_CCND1_Auxin6hrs-FF1-BinE-PCR4-Rep1_S293"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2024-06-01T01:43:06.764177+00:00",
"file_format": "fastq",
"file_size": 20814259,
"href": "/sequence-files/IGVFFI4198FZCC/@@download/IGVFFI4198FZCC.fastq.gz",
"md5sum": "aa313c12ba3093f2bc155eba188d8455",
"s3_uri": "s3://igvf-files/2024/06/01/7e0aaf75-9c01-4a0b-a7de-166b8da6c731/IGVFFI4198FZCC.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/CCND1-Auxin6hrs-FF1-BinE-PCR4-Rep1_S293_R1_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/configuration-files/IGVFFI8151RHFP/",
"accession": "IGVFFI8151RHFP",
"aliases": [
"jesse-engreitz:seqspecfile_CRUDO_CCND1_Auxin6hrs-FF1-BinE-PCR4-Rep1_S293"
],
"content_type": "seqspec",
"creation_timestamp": "2024-06-11T20:30:44.206699+00:00",
"file_format": "yaml",
"file_size": 914,
"href": "/configuration-files/IGVFFI8151RHFP/@@download/IGVFFI8151RHFP.yaml.gz",
"md5sum": "3fd0908ef71561338a4e778d611774b6",
"s3_uri": "s3://igvf-files/2024/06/11/750fa75e-922b-4f5a-8578-f6b0cee7e1f8/IGVFFI8151RHFP.yaml.gz",
"status": "released",
"submitted_file_name": "/oak/stanford/groups/engreitz/Projects/Cohesin/240410_IGVF_upload/seqspec/guideseq.out.CCND1_Auxin6hrs-FF1-BinE-PCR4-Rep1_S293.yaml",
"upload_status": "validation exempted"
},
{
"@id": "/sequence-files/IGVFFI5619AUER/",
"accession": "IGVFFI5619AUER",
"aliases": [
"jesse-engreitz:auxiliary_file_CRUDO_CCND1_Auxin6hrs-FF1-BinE-PCR3-Rep1_S287"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2024-06-01T01:42:46.956510+00:00",
"file_format": "fastq",
"file_size": 25749453,
"href": "/sequence-files/IGVFFI5619AUER/@@download/IGVFFI5619AUER.fastq.gz",
"md5sum": "54b2ecccfd5bba8eb499d52772aeec50",
"s3_uri": "s3://igvf-files/2024/06/01/0353b05e-c812-4aee-8d5d-3e2f9ef1a3cf/IGVFFI5619AUER.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/CCND1-Auxin6hrs-FF1-BinE-PCR3-Rep1_S287_R1_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI5866ZGPN/",
"accession": "IGVFFI5866ZGPN",
"aliases": [
"jesse-engreitz:auxiliary_file_CRUDO_CCND1_Auxin6hrs-FF1-BinE-PCR2-Rep1_S251"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2024-06-01T01:42:29.854353+00:00",
"file_format": "fastq",
"file_size": 13911957,
"href": "/sequence-files/IGVFFI5866ZGPN/@@download/IGVFFI5866ZGPN.fastq.gz",
"md5sum": "4963b7f1beb180de867afedf5a91b442",
"s3_uri": "s3://igvf-files/2024/06/01/cf0558d7-5a5b-4990-9754-770c102dd8a5/IGVFFI5866ZGPN.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/CCND1-Auxin6hrs-FF1-BinE-PCR2-Rep1_S251_R1_001.fastq.gz",
"upload_status": "validated"
}
],
"input_for": [
"/analysis-sets/IGVFDS1569RNPD/"
],
"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": "2024-07-10T19:39:21.978651+00:00",
"samples": [
{
"@id": "/in-vitro-systems/IGVFSM3721QHDS/",
"@type": [
"InVitroSystem",
"Biosample",
"Sample",
"Item"
],
"accession": "IGVFSM3721QHDS",
"aliases": [
"jesse-engreitz:in-vitro-system_CRUDO_CCND1_Auxin6hrs-FF1-BinE-PCR1-Rep1_S245",
"jesse-engreitz:in-vitro-system_CRUDO_CCND1_Auxin6hrs-FF1-BinE-PCR2-Rep1_S251",
"jesse-engreitz:in-vitro-system_CRUDO_CCND1_Auxin6hrs-FF1-BinE-PCR3-Rep1_S287",
"jesse-engreitz:in-vitro-system_CRUDO_CCND1_Auxin6hrs-FF1-BinE-PCR4-Rep1_S293"
],
"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 CCND1) 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": "2024-06-01T01:42:12.473543+00:00",
"summary": "mixed CRISPR FlowFISH screen sorted on the expression of CCND1 integrating a guide (sgRNA) library targeting accessible genome regions in many genomic loci",
"targeted_genes": [
{
"@id": "/genes/ENSG00000110092/",
"geneid": "ENSG00000110092",
"name": "cyclin D1",
"status": "released",
"symbol": "CCND1",
"synonyms": [
"U21B31",
"cyclin D1",
"B-cell CLL/lymphoma 1",
"PRAD1 oncogene",
"PRAD1",
"CCND1",
"G1/S-specific cyclin-D1",
"BCL-1 oncogene",
"BCL1",
"D11S287E",
"B-cell lymphoma 1 protein"
]
}
],
"uuid": "e85f2985-c3c6-4229-8610-3cf59ba0c394"
}