{
"@context": "/terms/",
"@id": "/measurement-sets/IGVFDS0528ZIOC/",
"@type": [
"MeasurementSet",
"FileSet",
"Item"
],
"accession": "IGVFDS0528ZIOC",
"aliases": [
"jesse-engreitz:measurement_CRUDO_CCND1_Auxin0hrs-FF1-BinC-PCR1-Rep1_S219",
"jesse-engreitz:measurement_CRUDO_CCND1_Auxin0hrs-FF1-BinC-PCR2-Rep1_S225",
"jesse-engreitz:measurement_CRUDO_CCND1_Auxin0hrs-FF1-BinC-PCR3-Rep1_S261",
"jesse-engreitz:measurement_CRUDO_CCND1_Auxin0hrs-FF1-BinC-PCR4-Rep1_S267"
],
"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 [IGVFSM2913DQHN](/in-vitro-systems/IGVFSM2913DQHN/) 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/IGVFSM2913DQHN/"
},
{
"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 [IGVFDS0528ZIOC](/measurement-sets/IGVFDS0528ZIOC/) 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/IGVFDS0528ZIOC/"
},
{
"category": "missing sequencing kit",
"detail": "Measurement set [IGVFDS0528ZIOC](/measurement-sets/IGVFDS0528ZIOC/) has sequence file(s) [IGVFFI0281SSVE](/sequence-files/IGVFFI0281SSVE/), [IGVFFI4666APET](/sequence-files/IGVFFI4666APET/), [IGVFFI6628DNUA](/sequence-files/IGVFFI6628DNUA/), [IGVFFI6676HNDS](/sequence-files/IGVFFI6676HNDS/) 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/IGVFDS0528ZIOC/"
}
],
"WARNING": [
{
"category": "missing nucleic acid delivery",
"detail": "In vitro system [IGVFSM2913DQHN](/in-vitro-systems/IGVFSM2913DQHN/) 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/IGVFSM2913DQHN/"
}
]
},
"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": "2024-05-13T22:07:23.634395+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/IGVFFI9157ATYV/",
"accession": "IGVFFI9157ATYV",
"aliases": [
"jesse-engreitz:seqspecfile_CRUDO_CCND1_Auxin0hrs-FF1-BinC-PCR3-Rep1_S261"
],
"content_type": "seqspec",
"creation_timestamp": "2024-06-11T20:28:31.944623+00:00",
"file_format": "yaml",
"file_size": 913,
"href": "/configuration-files/IGVFFI9157ATYV/@@download/IGVFFI9157ATYV.yaml.gz",
"md5sum": "70f2e7a868922e42261fafc4dcdf682c",
"s3_uri": "s3://igvf-files/2024/06/11/1a92a8ae-ac33-4857-b008-db0a40dd35f1/IGVFFI9157ATYV.yaml.gz",
"status": "released",
"submitted_file_name": "/oak/stanford/groups/engreitz/Projects/Cohesin/240410_IGVF_upload/seqspec/guideseq.out.CCND1_Auxin0hrs-FF1-BinC-PCR3-Rep1_S261.yaml",
"upload_status": "validation exempted"
},
{
"@id": "/configuration-files/IGVFFI9386BVXR/",
"accession": "IGVFFI9386BVXR",
"aliases": [
"jesse-engreitz:seqspecfile_CRUDO_CCND1_Auxin0hrs-FF1-BinC-PCR2-Rep1_S225"
],
"content_type": "seqspec",
"creation_timestamp": "2024-06-11T20:28:18.053492+00:00",
"file_format": "yaml",
"file_size": 912,
"href": "/configuration-files/IGVFFI9386BVXR/@@download/IGVFFI9386BVXR.yaml.gz",
"md5sum": "5a5d4ab7879cefc72ddaec8577b64ca6",
"s3_uri": "s3://igvf-files/2024/06/11/e0d94c4c-66cb-457b-b5dd-c4f7fee7c665/IGVFFI9386BVXR.yaml.gz",
"status": "released",
"submitted_file_name": "/oak/stanford/groups/engreitz/Projects/Cohesin/240410_IGVF_upload/seqspec/guideseq.out.CCND1_Auxin0hrs-FF1-BinC-PCR2-Rep1_S225.yaml",
"upload_status": "validation exempted"
},
{
"@id": "/configuration-files/IGVFFI0373UCGE/",
"accession": "IGVFFI0373UCGE",
"aliases": [
"jesse-engreitz:seqspecfile_CRUDO_CCND1_Auxin0hrs-FF1-BinC-PCR4-Rep1_S267"
],
"content_type": "seqspec",
"creation_timestamp": "2024-06-11T20:28:46.307088+00:00",
"file_format": "yaml",
"file_size": 913,
"href": "/configuration-files/IGVFFI0373UCGE/@@download/IGVFFI0373UCGE.yaml.gz",
"md5sum": "08df2a3b80bd03ed3bed75e75d70b118",
"s3_uri": "s3://igvf-files/2024/06/11/b99d0146-9044-4397-9818-4884b859d38d/IGVFFI0373UCGE.yaml.gz",
"status": "released",
"submitted_file_name": "/oak/stanford/groups/engreitz/Projects/Cohesin/240410_IGVF_upload/seqspec/guideseq.out.CCND1_Auxin0hrs-FF1-BinC-PCR4-Rep1_S267.yaml",
"upload_status": "validation exempted"
},
{
"@id": "/sequence-files/IGVFFI0281SSVE/",
"accession": "IGVFFI0281SSVE",
"aliases": [
"jesse-engreitz:auxiliary_file_CRUDO_CCND1_Auxin0hrs-FF1-BinC-PCR1-Rep1_S219"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2024-06-01T01:36:02.300105+00:00",
"file_format": "fastq",
"file_size": 23741843,
"href": "/sequence-files/IGVFFI0281SSVE/@@download/IGVFFI0281SSVE.fastq.gz",
"md5sum": "a30b686ab3124d0d417ea4bceeb48d54",
"s3_uri": "s3://igvf-files/2024/06/01/6b4ccd84-7aa2-4b21-b997-a6e772389b8d/IGVFFI0281SSVE.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-BinC-PCR1-Rep1_S219_R1_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/configuration-files/IGVFFI2850JSOK/",
"accession": "IGVFFI2850JSOK",
"aliases": [
"jesse-engreitz:seqspecfile_CRUDO_CCND1_Auxin0hrs-FF1-BinC-PCR1-Rep1_S219"
],
"content_type": "seqspec",
"creation_timestamp": "2024-06-11T20:28:03.099293+00:00",
"file_format": "yaml",
"file_size": 913,
"href": "/configuration-files/IGVFFI2850JSOK/@@download/IGVFFI2850JSOK.yaml.gz",
"md5sum": "a9028226c3692e3616f07ea32a02f0d7",
"s3_uri": "s3://igvf-files/2024/06/11/11202222-20d2-4ca4-a398-a6f5cf5b6f06/IGVFFI2850JSOK.yaml.gz",
"status": "released",
"submitted_file_name": "/oak/stanford/groups/engreitz/Projects/Cohesin/240410_IGVF_upload/seqspec/guideseq.out.CCND1_Auxin0hrs-FF1-BinC-PCR1-Rep1_S219.yaml",
"upload_status": "validation exempted"
},
{
"@id": "/sequence-files/IGVFFI4666APET/",
"accession": "IGVFFI4666APET",
"aliases": [
"jesse-engreitz:auxiliary_file_CRUDO_CCND1_Auxin0hrs-FF1-BinC-PCR2-Rep1_S225"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2024-06-01T01:36:20.061604+00:00",
"file_format": "fastq",
"file_size": 19586330,
"href": "/sequence-files/IGVFFI4666APET/@@download/IGVFFI4666APET.fastq.gz",
"md5sum": "cd27bcc61e81fdeb653b50fd899ca02a",
"s3_uri": "s3://igvf-files/2024/06/01/3655fc84-0222-4c07-89bb-87b14abae1cc/IGVFFI4666APET.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-BinC-PCR2-Rep1_S225_R1_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI6628DNUA/",
"accession": "IGVFFI6628DNUA",
"aliases": [
"jesse-engreitz:auxiliary_file_CRUDO_CCND1_Auxin0hrs-FF1-BinC-PCR3-Rep1_S261"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2024-06-01T01:36:38.439911+00:00",
"file_format": "fastq",
"file_size": 23792398,
"href": "/sequence-files/IGVFFI6628DNUA/@@download/IGVFFI6628DNUA.fastq.gz",
"md5sum": "5d1f511721054dbaaaea7796f44f0751",
"s3_uri": "s3://igvf-files/2024/06/01/1fe08c33-546f-47cc-95e7-aef43a5ea15c/IGVFFI6628DNUA.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-BinC-PCR3-Rep1_S261_R1_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI6676HNDS/",
"accession": "IGVFFI6676HNDS",
"aliases": [
"jesse-engreitz:auxiliary_file_CRUDO_CCND1_Auxin0hrs-FF1-BinC-PCR4-Rep1_S267"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2024-06-01T01:36:56.673095+00:00",
"file_format": "fastq",
"file_size": 27428664,
"href": "/sequence-files/IGVFFI6676HNDS/@@download/IGVFFI6676HNDS.fastq.gz",
"md5sum": "ce90f066cb121dec2f0b45c830310f00",
"s3_uri": "s3://igvf-files/2024/06/01/fbe1f7cc-4ab5-44c6-9e89-784e9759a86b/IGVFFI6676HNDS.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-BinC-PCR4-Rep1_S267_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": "2024-07-10T19:38:22.799467+00:00",
"samples": [
{
"@id": "/in-vitro-systems/IGVFSM2913DQHN/",
"@type": [
"InVitroSystem",
"Biosample",
"Sample",
"Item"
],
"accession": "IGVFSM2913DQHN",
"aliases": [
"jesse-engreitz:in-vitro-system_CRUDO_CCND1_Auxin0hrs-FF1-BinC-PCR1-Rep1_S219",
"jesse-engreitz:in-vitro-system_CRUDO_CCND1_Auxin0hrs-FF1-BinC-PCR2-Rep1_S225",
"jesse-engreitz:in-vitro-system_CRUDO_CCND1_Auxin0hrs-FF1-BinC-PCR3-Rep1_S261",
"jesse-engreitz:in-vitro-system_CRUDO_CCND1_Auxin0hrs-FF1-BinC-PCR4-Rep1_S267"
],
"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 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": "2024-06-01T01:36:02.300105+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": "07af3911-7616-4746-a6e1-faca889a3da2"
}