{
"@context": "/terms/",
"@id": "/measurement-sets/IGVFDS2949NCKP/",
"@type": [
"MeasurementSet",
"FileSet",
"Item"
],
"accession": "IGVFDS2949NCKP",
"aliases": [
"jesse-engreitz:measurement_CRUDO_CCND1_Auxin0hrs-FF2-BinD-PCR1-Rep1_S232",
"jesse-engreitz:measurement_CRUDO_CCND1_Auxin0hrs-FF2-BinD-PCR2-Rep1_S238",
"jesse-engreitz:measurement_CRUDO_CCND1_Auxin0hrs-FF2-BinD-PCR3-Rep1_S274",
"jesse-engreitz:measurement_CRUDO_CCND1_Auxin0hrs-FF2-BinD-PCR4-Rep1_S280"
],
"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 [IGVFSM9888RFRZ](/in-vitro-systems/IGVFSM9888RFRZ/) 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/IGVFSM9888RFRZ/"
},
{
"category": "missing publication",
"detail": "Auxiliary set [IGVFDS1549RKIJ](/auxiliary-sets/IGVFDS1549RKIJ/) 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/IGVFDS1549RKIJ/"
},
{
"category": "missing publication",
"detail": "Measurement set [IGVFDS2949NCKP](/measurement-sets/IGVFDS2949NCKP/) 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/IGVFDS2949NCKP/"
},
{
"category": "missing sequencing kit",
"detail": "Measurement set [IGVFDS2949NCKP](/measurement-sets/IGVFDS2949NCKP/) has sequence file(s) [IGVFFI7774KVKB](/sequence-files/IGVFFI7774KVKB/), [IGVFFI9017LLWY](/sequence-files/IGVFFI9017LLWY/), [IGVFFI6030SAOG](/sequence-files/IGVFFI6030SAOG/), [IGVFFI8172OMRE](/sequence-files/IGVFFI8172OMRE/) 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/IGVFDS2949NCKP/"
}
],
"WARNING": [
{
"category": "missing nucleic acid delivery",
"detail": "In vitro system [IGVFSM9888RFRZ](/in-vitro-systems/IGVFSM9888RFRZ/) 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/IGVFSM9888RFRZ/"
}
]
},
"auxiliary_sets": [
{
"@id": "/auxiliary-sets/IGVFDS1549RKIJ/",
"accession": "IGVFDS1549RKIJ",
"aliases": [
"jesse-engreitz:auxiliary_sortparams_CRUDO_CCND1_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/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": "2024-05-13T22:07:48.825280+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/IGVFFI7108WMVT/",
"accession": "IGVFFI7108WMVT",
"aliases": [
"jesse-engreitz:seqspecfile_CRUDO_CCND1_Auxin0hrs-FF2-BinD-PCR2-Rep1_S238"
],
"content_type": "seqspec",
"creation_timestamp": "2024-06-11T20:29:17.307762+00:00",
"file_format": "yaml",
"file_size": 914,
"href": "/configuration-files/IGVFFI7108WMVT/@@download/IGVFFI7108WMVT.yaml.gz",
"md5sum": "6223b1606a25faa9f2dd523a1d4f24be",
"s3_uri": "s3://igvf-files/2024/06/11/021d990e-97f0-4ac5-902c-a9c4e080ec75/IGVFFI7108WMVT.yaml.gz",
"status": "released",
"submitted_file_name": "/oak/stanford/groups/engreitz/Projects/Cohesin/240410_IGVF_upload/seqspec/guideseq.out.CCND1_Auxin0hrs-FF2-BinD-PCR2-Rep1_S238.yaml",
"upload_status": "validation exempted"
},
{
"@id": "/configuration-files/IGVFFI3301LAMU/",
"accession": "IGVFFI3301LAMU",
"aliases": [
"jesse-engreitz:seqspecfile_CRUDO_CCND1_Auxin0hrs-FF2-BinD-PCR1-Rep1_S232"
],
"content_type": "seqspec",
"creation_timestamp": "2024-06-11T20:29:03.395319+00:00",
"file_format": "yaml",
"file_size": 915,
"href": "/configuration-files/IGVFFI3301LAMU/@@download/IGVFFI3301LAMU.yaml.gz",
"md5sum": "6ee29302e883ef96a0e7d79d39107da3",
"s3_uri": "s3://igvf-files/2024/06/11/e136e748-bcda-41c1-946b-f1991edb189a/IGVFFI3301LAMU.yaml.gz",
"status": "released",
"submitted_file_name": "/oak/stanford/groups/engreitz/Projects/Cohesin/240410_IGVF_upload/seqspec/guideseq.out.CCND1_Auxin0hrs-FF2-BinD-PCR1-Rep1_S232.yaml",
"upload_status": "validation exempted"
},
{
"@id": "/configuration-files/IGVFFI7568TJSW/",
"accession": "IGVFFI7568TJSW",
"aliases": [
"jesse-engreitz:seqspecfile_CRUDO_CCND1_Auxin0hrs-FF2-BinD-PCR4-Rep1_S280"
],
"content_type": "seqspec",
"creation_timestamp": "2024-06-11T20:29:45.264881+00:00",
"file_format": "yaml",
"file_size": 914,
"href": "/configuration-files/IGVFFI7568TJSW/@@download/IGVFFI7568TJSW.yaml.gz",
"md5sum": "bd14044b3dc1b89b3e97e5469a400d5f",
"s3_uri": "s3://igvf-files/2024/06/11/248276f3-e5c5-42db-b72d-10163dd224b6/IGVFFI7568TJSW.yaml.gz",
"status": "released",
"submitted_file_name": "/oak/stanford/groups/engreitz/Projects/Cohesin/240410_IGVF_upload/seqspec/guideseq.out.CCND1_Auxin0hrs-FF2-BinD-PCR4-Rep1_S280.yaml",
"upload_status": "validation exempted"
},
{
"@id": "/configuration-files/IGVFFI9558UYBL/",
"accession": "IGVFFI9558UYBL",
"aliases": [
"jesse-engreitz:seqspecfile_CRUDO_CCND1_Auxin0hrs-FF2-BinD-PCR3-Rep1_S274"
],
"content_type": "seqspec",
"creation_timestamp": "2024-06-11T20:29:31.272162+00:00",
"file_format": "yaml",
"file_size": 912,
"href": "/configuration-files/IGVFFI9558UYBL/@@download/IGVFFI9558UYBL.yaml.gz",
"md5sum": "e8b07f050b74b6647a0f28c9e2da0edc",
"s3_uri": "s3://igvf-files/2024/06/11/987616fe-7d14-4324-9ad0-77ae7de1bd76/IGVFFI9558UYBL.yaml.gz",
"status": "released",
"submitted_file_name": "/oak/stanford/groups/engreitz/Projects/Cohesin/240410_IGVF_upload/seqspec/guideseq.out.CCND1_Auxin0hrs-FF2-BinD-PCR3-Rep1_S274.yaml",
"upload_status": "validation exempted"
},
{
"@id": "/sequence-files/IGVFFI7774KVKB/",
"accession": "IGVFFI7774KVKB",
"aliases": [
"jesse-engreitz:auxiliary_file_CRUDO_CCND1_Auxin0hrs-FF2-BinD-PCR2-Rep1_S238"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2024-06-01T01:37:35.348521+00:00",
"file_format": "fastq",
"file_size": 18935065,
"href": "/sequence-files/IGVFFI7774KVKB/@@download/IGVFFI7774KVKB.fastq.gz",
"md5sum": "54ef96411603a0729aaa0a61592d9b0e",
"s3_uri": "s3://igvf-files/2024/06/01/c96f8bd5-5c9f-4e8f-bbfc-5e9b913555f5/IGVFFI7774KVKB.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-FF2-BinD-PCR2-Rep1_S238_R1_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI9017LLWY/",
"accession": "IGVFFI9017LLWY",
"aliases": [
"jesse-engreitz:auxiliary_file_CRUDO_CCND1_Auxin0hrs-FF2-BinD-PCR1-Rep1_S232"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2024-06-01T01:37:17.550617+00:00",
"file_format": "fastq",
"file_size": 19145096,
"href": "/sequence-files/IGVFFI9017LLWY/@@download/IGVFFI9017LLWY.fastq.gz",
"md5sum": "2cbdd6934ebd858426d5b241073d99d9",
"s3_uri": "s3://igvf-files/2024/06/01/f76e5b80-83be-451f-af1c-c2e12a4ea06c/IGVFFI9017LLWY.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-FF2-BinD-PCR1-Rep1_S232_R1_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI6030SAOG/",
"accession": "IGVFFI6030SAOG",
"aliases": [
"jesse-engreitz:auxiliary_file_CRUDO_CCND1_Auxin0hrs-FF2-BinD-PCR3-Rep1_S274"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2024-06-01T01:37:53.123405+00:00",
"file_format": "fastq",
"file_size": 24245776,
"href": "/sequence-files/IGVFFI6030SAOG/@@download/IGVFFI6030SAOG.fastq.gz",
"md5sum": "26dbd294bf4afbc49cd2446a23d245f5",
"s3_uri": "s3://igvf-files/2024/06/01/93a6bfd4-f546-4268-9d4c-36e2eb5dedc5/IGVFFI6030SAOG.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-FF2-BinD-PCR3-Rep1_S274_R1_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI8172OMRE/",
"accession": "IGVFFI8172OMRE",
"aliases": [
"jesse-engreitz:auxiliary_file_CRUDO_CCND1_Auxin0hrs-FF2-BinD-PCR4-Rep1_S280"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2024-06-01T01:38:15.440089+00:00",
"file_format": "fastq",
"file_size": 24490365,
"href": "/sequence-files/IGVFFI8172OMRE/@@download/IGVFFI8172OMRE.fastq.gz",
"md5sum": "f3dcfc5c20643a1dd38f2d87c2ce2f3f",
"s3_uri": "s3://igvf-files/2024/06/01/5df06ec8-2c66-4755-82ca-33d90a801d29/IGVFFI8172OMRE.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-FF2-BinD-PCR4-Rep1_S280_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": "2024-07-10T19:38:51.691026+00:00",
"samples": [
{
"@id": "/in-vitro-systems/IGVFSM9888RFRZ/",
"@type": [
"InVitroSystem",
"Biosample",
"Sample",
"Item"
],
"accession": "IGVFSM9888RFRZ",
"aliases": [
"jesse-engreitz:in-vitro-system_CRUDO_CCND1_Auxin0hrs-FF2-BinD-PCR1-Rep1_S232",
"jesse-engreitz:in-vitro-system_CRUDO_CCND1_Auxin0hrs-FF2-BinD-PCR2-Rep1_S238",
"jesse-engreitz:in-vitro-system_CRUDO_CCND1_Auxin0hrs-FF2-BinD-PCR3-Rep1_S274",
"jesse-engreitz:in-vitro-system_CRUDO_CCND1_Auxin0hrs-FF2-BinD-PCR4-Rep1_S280"
],
"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 D for 55-65% 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": "2024-06-01T01:37:17.550617+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": "33efe0ae-dc3c-40f0-8b29-ddba6d6d22d1"
}