{
"@context": "/terms/",
"@id": "/measurement-sets/IGVFDS2241NBBY/",
"@type": [
"MeasurementSet",
"FileSet",
"Item"
],
"accession": "IGVFDS2241NBBY",
"aliases": [
"jesse-engreitz:measurement_CRUDO_CCND1_Auxin0hrs-FF1-BinF-PCR1-Rep1_S222",
"jesse-engreitz:measurement_CRUDO_CCND1_Auxin0hrs-FF1-BinF-PCR2-Rep1_S228",
"jesse-engreitz:measurement_CRUDO_CCND1_Auxin0hrs-FF1-BinF-PCR3-Rep1_S264",
"jesse-engreitz:measurement_CRUDO_CCND1_Auxin0hrs-FF1-BinF-PCR4-Rep1_S270"
],
"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": "In vitro system [IGVFSM4218VHTT](/in-vitro-systems/IGVFSM4218VHTT/) 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/IGVFSM4218VHTT/"
},
{
"category": "missing publication",
"detail": "Auxiliary set [IGVFDS5464XLTY](/auxiliary-sets/IGVFDS5464XLTY/) 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/IGVFDS5464XLTY/"
},
{
"category": "missing publication",
"detail": "Measurement set [IGVFDS2241NBBY](/measurement-sets/IGVFDS2241NBBY/) 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/IGVFDS2241NBBY/"
},
{
"category": "missing sequencing kit",
"detail": "Measurement set [IGVFDS2241NBBY](/measurement-sets/IGVFDS2241NBBY/) has sequence file(s) [IGVFFI9279HEMN](/sequence-files/IGVFFI9279HEMN/), [IGVFFI8918ZHNH](/sequence-files/IGVFFI8918ZHNH/), [IGVFFI6818RKHX](/sequence-files/IGVFFI6818RKHX/), [IGVFFI5127EQNC](/sequence-files/IGVFFI5127EQNC/) 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/IGVFDS2241NBBY/"
}
],
"WARNING": [
{
"category": "missing nucleic acid delivery",
"detail": "In vitro system [IGVFSM4218VHTT](/in-vitro-systems/IGVFSM4218VHTT/) 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/IGVFSM4218VHTT/"
}
]
},
"auxiliary_sets": [
{
"@id": "/auxiliary-sets/IGVFDS5464XLTY/",
"accession": "IGVFDS5464XLTY",
"aliases": [
"jesse-engreitz:auxiliary_sortparams_CRUDO_CCND1_Auxin0hrs-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": "2024-05-13T22:07:26.478631+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/IGVFFI8036KMXA/",
"accession": "IGVFFI8036KMXA",
"aliases": [
"jesse-engreitz:seqspecfile_CRUDO_CCND1_Auxin0hrs-FF1-BinF-PCR4-Rep1_S270"
],
"content_type": "seqspec",
"creation_timestamp": "2024-06-11T20:28:53.325992+00:00",
"file_format": "yaml",
"file_size": 913,
"href": "/configuration-files/IGVFFI8036KMXA/@@download/IGVFFI8036KMXA.yaml.gz",
"md5sum": "3a0d4d63a628c5dc8a4e09dbfc5c2fa1",
"s3_uri": "s3://igvf-files/2024/06/11/d6890866-6e0a-4344-902e-a14df883ab32/IGVFFI8036KMXA.yaml.gz",
"status": "released",
"submitted_file_name": "/oak/stanford/groups/engreitz/Projects/Cohesin/240410_IGVF_upload/seqspec/guideseq.out.CCND1_Auxin0hrs-FF1-BinF-PCR4-Rep1_S270.yaml",
"upload_status": "validation exempted"
},
{
"@id": "/configuration-files/IGVFFI4912PNJI/",
"accession": "IGVFFI4912PNJI",
"aliases": [
"jesse-engreitz:seqspecfile_CRUDO_CCND1_Auxin0hrs-FF1-BinF-PCR3-Rep1_S264"
],
"content_type": "seqspec",
"creation_timestamp": "2024-06-11T20:28:38.680666+00:00",
"file_format": "yaml",
"file_size": 915,
"href": "/configuration-files/IGVFFI4912PNJI/@@download/IGVFFI4912PNJI.yaml.gz",
"md5sum": "d26daaa89bd6a7958912f8165e76b898",
"s3_uri": "s3://igvf-files/2024/06/11/9fc64df1-490b-4bd8-aea0-fbfe7f3bffb0/IGVFFI4912PNJI.yaml.gz",
"status": "released",
"submitted_file_name": "/oak/stanford/groups/engreitz/Projects/Cohesin/240410_IGVF_upload/seqspec/guideseq.out.CCND1_Auxin0hrs-FF1-BinF-PCR3-Rep1_S264.yaml",
"upload_status": "validation exempted"
},
{
"@id": "/configuration-files/IGVFFI6107TILF/",
"accession": "IGVFFI6107TILF",
"aliases": [
"jesse-engreitz:seqspecfile_CRUDO_CCND1_Auxin0hrs-FF1-BinF-PCR2-Rep1_S228"
],
"content_type": "seqspec",
"creation_timestamp": "2024-06-11T20:28:24.942247+00:00",
"file_format": "yaml",
"file_size": 915,
"href": "/configuration-files/IGVFFI6107TILF/@@download/IGVFFI6107TILF.yaml.gz",
"md5sum": "adf51fb34058f704b9d955f2e533da90",
"s3_uri": "s3://igvf-files/2024/06/11/4f62228a-aca6-40d8-8d41-00996aed29b2/IGVFFI6107TILF.yaml.gz",
"status": "released",
"submitted_file_name": "/oak/stanford/groups/engreitz/Projects/Cohesin/240410_IGVF_upload/seqspec/guideseq.out.CCND1_Auxin0hrs-FF1-BinF-PCR2-Rep1_S228.yaml",
"upload_status": "validation exempted"
},
{
"@id": "/configuration-files/IGVFFI7078QGHI/",
"accession": "IGVFFI7078QGHI",
"aliases": [
"jesse-engreitz:seqspecfile_CRUDO_CCND1_Auxin0hrs-FF1-BinF-PCR1-Rep1_S222"
],
"content_type": "seqspec",
"creation_timestamp": "2024-06-11T20:28:10.610396+00:00",
"file_format": "yaml",
"file_size": 914,
"href": "/configuration-files/IGVFFI7078QGHI/@@download/IGVFFI7078QGHI.yaml.gz",
"md5sum": "aea6ed8b1b475a78049d850987c52769",
"s3_uri": "s3://igvf-files/2024/06/11/ed3816b8-b038-4028-a347-9072a35cabf4/IGVFFI7078QGHI.yaml.gz",
"status": "released",
"submitted_file_name": "/oak/stanford/groups/engreitz/Projects/Cohesin/240410_IGVF_upload/seqspec/guideseq.out.CCND1_Auxin0hrs-FF1-BinF-PCR1-Rep1_S222.yaml",
"upload_status": "validation exempted"
},
{
"@id": "/sequence-files/IGVFFI9279HEMN/",
"accession": "IGVFFI9279HEMN",
"aliases": [
"jesse-engreitz:auxiliary_file_CRUDO_CCND1_Auxin0hrs-FF1-BinF-PCR1-Rep1_S222"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2024-06-01T01:36:11.253477+00:00",
"file_format": "fastq",
"file_size": 19329587,
"href": "/sequence-files/IGVFFI9279HEMN/@@download/IGVFFI9279HEMN.fastq.gz",
"md5sum": "9c3397faab6cc843d6d752c4715a9102",
"s3_uri": "s3://igvf-files/2024/06/01/7d8fbe0f-86c5-4530-9425-f83d600a47e2/IGVFFI9279HEMN.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-Auxin0hrs-FF1-BinF-PCR1-Rep1_S222_R1_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI8918ZHNH/",
"accession": "IGVFFI8918ZHNH",
"aliases": [
"jesse-engreitz:auxiliary_file_CRUDO_CCND1_Auxin0hrs-FF1-BinF-PCR3-Rep1_S264"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2024-06-01T01:36:47.423039+00:00",
"file_format": "fastq",
"file_size": 26679582,
"href": "/sequence-files/IGVFFI8918ZHNH/@@download/IGVFFI8918ZHNH.fastq.gz",
"md5sum": "8691691b4bf61c638a500c5f6ab3d7ad",
"s3_uri": "s3://igvf-files/2024/06/01/b7a3d7f6-31b9-450a-b06a-32c1659788cd/IGVFFI8918ZHNH.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-Auxin0hrs-FF1-BinF-PCR3-Rep1_S264_R1_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI6818RKHX/",
"accession": "IGVFFI6818RKHX",
"aliases": [
"jesse-engreitz:auxiliary_file_CRUDO_CCND1_Auxin0hrs-FF1-BinF-PCR2-Rep1_S228"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2024-06-01T01:36:29.478680+00:00",
"file_format": "fastq",
"file_size": 19083131,
"href": "/sequence-files/IGVFFI6818RKHX/@@download/IGVFFI6818RKHX.fastq.gz",
"md5sum": "e9223dfb38f2e0343841f901386a0852",
"s3_uri": "s3://igvf-files/2024/06/01/ed435d61-e851-4e66-badf-b37a5d08ee8c/IGVFFI6818RKHX.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-Auxin0hrs-FF1-BinF-PCR2-Rep1_S228_R1_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI5127EQNC/",
"accession": "IGVFFI5127EQNC",
"aliases": [
"jesse-engreitz:auxiliary_file_CRUDO_CCND1_Auxin0hrs-FF1-BinF-PCR4-Rep1_S270"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2024-06-01T01:37:05.555898+00:00",
"file_format": "fastq",
"file_size": 12550088,
"href": "/sequence-files/IGVFFI5127EQNC/@@download/IGVFFI5127EQNC.fastq.gz",
"md5sum": "904f4654d393a2533efc9a9c9d20bdc5",
"s3_uri": "s3://igvf-files/2024/06/01/0052ecf9-7420-446f-a14c-ea29b860250d/IGVFFI5127EQNC.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-Auxin0hrs-FF1-BinF-PCR4-Rep1_S270_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": "2024-07-10T19:38:35.233109+00:00",
"samples": [
{
"@id": "/in-vitro-systems/IGVFSM4218VHTT/",
"@type": [
"InVitroSystem",
"Biosample",
"Sample",
"Item"
],
"accession": "IGVFSM4218VHTT",
"aliases": [
"jesse-engreitz:in-vitro-system_CRUDO_CCND1_Auxin0hrs-FF1-BinF-PCR1-Rep1_S222",
"jesse-engreitz:in-vitro-system_CRUDO_CCND1_Auxin0hrs-FF1-BinF-PCR2-Rep1_S228",
"jesse-engreitz:in-vitro-system_CRUDO_CCND1_Auxin0hrs-FF1-BinF-PCR3-Rep1_S264",
"jesse-engreitz:in-vitro-system_CRUDO_CCND1_Auxin0hrs-FF1-BinF-PCR4-Rep1_S270"
],
"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 F for 80-100% expression of CCND1) 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": "2024-06-01T01:36:11.253477+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": "90b54b14-ca57-47a3-b062-10ad062d8a9e"
}