{
"@context": "/terms/",
"@id": "/measurement-sets/IGVFDS6224TNVO/",
"@type": [
"MeasurementSet",
"FileSet",
"Item"
],
"accession": "IGVFDS6224TNVO",
"aliases": [
"jesse-engreitz:measurement_CRUDO_MYC-Auxin0hrs-FF2-BinF-PCR1_Rep1_S30",
"jesse-engreitz:measurement_CRUDO_MYC-Auxin0hrs-FF2-BinF-PCR1_Rep2_S85",
"jesse-engreitz:measurement_CRUDO_MYC-Auxin0hrs-FF2-BinF-PCR2_Rep1_S36",
"jesse-engreitz:measurement_CRUDO_MYC-Auxin0hrs-FF2-BinF-PCR2_Rep2_S91",
"jesse-engreitz:measurement_CRUDO_MYC-Auxin0hrs-FF2-BinF-PCR3_Rep1_S42",
"jesse-engreitz:measurement_CRUDO_MYC-Auxin0hrs-FF2-BinF-PCR3_Rep2_S97",
"jesse-engreitz:measurement_CRUDO_MYC-Auxin0hrs-FF2-BinF-PCR4_Rep1_S48",
"jesse-engreitz:measurement_CRUDO_MYC-Auxin0hrs-FF2-BinF-PCR4_Rep2_S103"
],
"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 [IGVFSM9724UBWS](/in-vitro-systems/IGVFSM9724UBWS/) 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/IGVFSM9724UBWS/"
},
{
"category": "missing publication",
"detail": "Measurement set [IGVFDS6224TNVO](/measurement-sets/IGVFDS6224TNVO/) 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/IGVFDS6224TNVO/"
},
{
"category": "missing sequencing kit",
"detail": "Measurement set [IGVFDS6224TNVO](/measurement-sets/IGVFDS6224TNVO/) has sequence file(s) [IGVFFI4236ZKZQ](/sequence-files/IGVFFI4236ZKZQ/), [IGVFFI0849URVD](/sequence-files/IGVFFI0849URVD/), [IGVFFI8775RJJR](/sequence-files/IGVFFI8775RJJR/), [IGVFFI8620KXPV](/sequence-files/IGVFFI8620KXPV/), [IGVFFI4472ZCED](/sequence-files/IGVFFI4472ZCED/), [IGVFFI6708LGQK](/sequence-files/IGVFFI6708LGQK/), [IGVFFI5078FJXF](/sequence-files/IGVFFI5078FJXF/), [IGVFFI8897HGJW](/sequence-files/IGVFFI8897HGJW/) 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/IGVFDS6224TNVO/"
},
{
"category": "missing publication",
"detail": "Auxiliary set [IGVFDS8214HXSU](/auxiliary-sets/IGVFDS8214HXSU/) 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/IGVFDS8214HXSU/"
}
],
"WARNING": [
{
"category": "missing nucleic acid delivery",
"detail": "In vitro system [IGVFSM9724UBWS](/in-vitro-systems/IGVFSM9724UBWS/) 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/IGVFSM9724UBWS/"
}
]
},
"auxiliary_sets": [
{
"@id": "/auxiliary-sets/IGVFDS8214HXSU/",
"accession": "IGVFDS8214HXSU",
"aliases": [
"jesse-engreitz:auxiliary_sortparams_CRUDO_MYC-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"
},
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{
"@id": "/construct-library-sets/IGVFDS7857SYCK/",
"accession": "IGVFDS7857SYCK",
"file_set_type": "guide library",
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{
"@id": "/tabular-files/IGVFFI3782KCTX/",
"accession": "IGVFFI3782KCTX",
"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": "2024-05-21T17:16:14.763608+00:00",
"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",
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{
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"accession": "IGVFFI4236ZKZQ",
"aliases": [
"jesse-engreitz:auxiliary_file_CRUDO_MYC-Auxin0hrs-FF2-BinF-PCR2_Rep2_S91"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2024-06-01T02:02:08.041838+00:00",
"file_format": "fastq",
"file_size": 22199527,
"href": "/sequence-files/IGVFFI4236ZKZQ/@@download/IGVFFI4236ZKZQ.fastq.gz",
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"sequencing_platform": {
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"status": "released",
"term_name": "Illumina HiSeq 2500"
},
"status": "released",
"submitted_file_name": "/oak/stanford/groups/engreitz/Projects/Cohesin/220819B015_MYC/fastq_trim/MYC-Auxin0hrs-FF2-BinF-PCR2-Rep2_S91_R1_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/configuration-files/IGVFFI5121TSVZ/",
"accession": "IGVFFI5121TSVZ",
"aliases": [
"jesse-engreitz:seqspecfile_CRUDO_MYC-Auxin0hrs-FF2-BinF-PCR4_Rep2_S103"
],
"content_type": "seqspec",
"creation_timestamp": "2024-06-11T20:49:18.599630+00:00",
"file_format": "yaml",
"file_size": 912,
"href": "/configuration-files/IGVFFI5121TSVZ/@@download/IGVFFI5121TSVZ.yaml.gz",
"s3_uri": "s3://igvf-files/2024/06/11/fcc7a8c2-ea9c-4df4-a85c-4cbd37b32c41/IGVFFI5121TSVZ.yaml.gz",
"status": "released",
"submitted_file_name": "/oak/stanford/groups/engreitz/Projects/Cohesin/240410_IGVF_upload/seqspec/guideseq.out.MYC-Auxin0hrs-FF2-BinF-PCR4_Rep2_S103.yaml",
"upload_status": "validation exempted"
},
{
"@id": "/configuration-files/IGVFFI3084HVWV/",
"accession": "IGVFFI3084HVWV",
"aliases": [
"jesse-engreitz:seqspecfile_CRUDO_MYC-Auxin0hrs-FF2-BinF-PCR3_Rep1_S42"
],
"content_type": "seqspec",
"creation_timestamp": "2024-06-11T20:48:34.613676+00:00",
"file_format": "yaml",
"file_size": 910,
"href": "/configuration-files/IGVFFI3084HVWV/@@download/IGVFFI3084HVWV.yaml.gz",
"s3_uri": "s3://igvf-files/2024/06/11/2d9ed375-e864-4164-a606-61f265e380ce/IGVFFI3084HVWV.yaml.gz",
"status": "released",
"submitted_file_name": "/oak/stanford/groups/engreitz/Projects/Cohesin/240410_IGVF_upload/seqspec/guideseq.out.MYC-Auxin0hrs-FF2-BinF-PCR3_Rep1_S42.yaml",
"upload_status": "validation exempted"
},
{
"@id": "/configuration-files/IGVFFI6042PRCO/",
"accession": "IGVFFI6042PRCO",
"aliases": [
"jesse-engreitz:seqspecfile_CRUDO_MYC-Auxin0hrs-FF2-BinF-PCR1_Rep2_S85"
],
"content_type": "seqspec",
"creation_timestamp": "2024-06-11T20:47:51.464333+00:00",
"file_format": "yaml",
"file_size": 911,
"href": "/configuration-files/IGVFFI6042PRCO/@@download/IGVFFI6042PRCO.yaml.gz",
"s3_uri": "s3://igvf-files/2024/06/11/df76f6fc-93c1-4cf8-b3f4-fbd982e39f71/IGVFFI6042PRCO.yaml.gz",
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"upload_status": "validation exempted"
},
{
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"aliases": [
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],
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"creation_timestamp": "2024-06-11T20:48:48.880836+00:00",
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"file_size": 911,
"href": "/configuration-files/IGVFFI7674FVAU/@@download/IGVFFI7674FVAU.yaml.gz",
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"upload_status": "validation exempted"
},
{
"@id": "/configuration-files/IGVFFI5346CYNH/",
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"aliases": [
"jesse-engreitz:seqspecfile_CRUDO_MYC-Auxin0hrs-FF2-BinF-PCR4_Rep1_S48"
],
"content_type": "seqspec",
"creation_timestamp": "2024-06-11T20:49:03.715374+00:00",
"file_format": "yaml",
"file_size": 912,
"href": "/configuration-files/IGVFFI5346CYNH/@@download/IGVFFI5346CYNH.yaml.gz",
"s3_uri": "s3://igvf-files/2024/06/11/60b1ac54-ffac-479d-8f00-40bd63bc273d/IGVFFI5346CYNH.yaml.gz",
"status": "released",
"submitted_file_name": "/oak/stanford/groups/engreitz/Projects/Cohesin/240410_IGVF_upload/seqspec/guideseq.out.MYC-Auxin0hrs-FF2-BinF-PCR4_Rep1_S48.yaml",
"upload_status": "validation exempted"
},
{
"@id": "/sequence-files/IGVFFI0849URVD/",
"accession": "IGVFFI0849URVD",
"aliases": [
"jesse-engreitz:auxiliary_file_CRUDO_MYC-Auxin0hrs-FF2-BinF-PCR2_Rep1_S36"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2024-06-01T02:01:47.291416+00:00",
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"href": "/sequence-files/IGVFFI0849URVD/@@download/IGVFFI0849URVD.fastq.gz",
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"upload_status": "validated"
},
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"creation_timestamp": "2024-06-11T20:48:06.204925+00:00",
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"href": "/configuration-files/IGVFFI1174FSAA/@@download/IGVFFI1174FSAA.yaml.gz",
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},
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"@id": "/configuration-files/IGVFFI1820NGCT/",
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],
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},
{
"@id": "/configuration-files/IGVFFI4839KCLK/",
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},
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},
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},
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},
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],
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},
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},
"status": "released",
"submitted_file_name": "/oak/stanford/groups/engreitz/Projects/Cohesin/220819B015_MYC/fastq_trim/MYC-Auxin0hrs-FF2-BinF-PCR1-Rep2_S85_R1_001.fastq.gz",
"upload_status": "validated"
}
],
"input_for": [
"/analysis-sets/IGVFDS4544YEQM/"
],
"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": "2024-07-10T19:47:30.300819+00:00",
"samples": [
{
"@id": "/in-vitro-systems/IGVFSM9724UBWS/",
"@type": [
"InVitroSystem",
"Biosample",
"Sample",
"Item"
],
"accession": "IGVFSM9724UBWS",
"aliases": [
"jesse-engreitz:in-vitro-system_CRUDO_MYC-Auxin0hrs-FF2-BinF-PCR1_Rep1_S30",
"jesse-engreitz:in-vitro-system_CRUDO_MYC-Auxin0hrs-FF2-BinF-PCR1_Rep2_S85",
"jesse-engreitz:in-vitro-system_CRUDO_MYC-Auxin0hrs-FF2-BinF-PCR2_Rep1_S36",
"jesse-engreitz:in-vitro-system_CRUDO_MYC-Auxin0hrs-FF2-BinF-PCR2_Rep2_S91",
"jesse-engreitz:in-vitro-system_CRUDO_MYC-Auxin0hrs-FF2-BinF-PCR3_Rep1_S42",
"jesse-engreitz:in-vitro-system_CRUDO_MYC-Auxin0hrs-FF2-BinF-PCR3_Rep2_S97",
"jesse-engreitz:in-vitro-system_CRUDO_MYC-Auxin0hrs-FF2-BinF-PCR4_Rep1_S48",
"jesse-engreitz:in-vitro-system_CRUDO_MYC-Auxin0hrs-FF2-BinF-PCR4_Rep2_S103"
],
"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 MYC) 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": "2024-06-01T02:01:02.263131+00:00",
"summary": "mixed CRISPR FlowFISH screen sorted on the expression of MYC integrating a guide (sgRNA) library targeting accessible genome regions in many genomic loci",
"targeted_genes": [
{
"@id": "/genes/ENSG00000136997/",
"geneid": "ENSG00000136997",
"name": "MYC proto-oncogene, bHLH transcription factor",
"status": "released",
"symbol": "MYC",
"synonyms": [
"bHLHe39",
"myc-related translation/localization regulatory factor",
"MYC proto-oncogene, bHLH transcription factor",
"MYC",
"c-Myc",
"v-myc avian myelocytomatosis viral oncogene homolog",
"proto-oncogene c-Myc",
"transcription factor p64",
"myc proto-oncogene protein",
"avian myelocytomatosis viral oncogene homolog",
"MRTL",
"class E basic helix-loop-helix protein 39",
"MYCC",
"v-myc myelocytomatosis viral oncogene homolog"
]
}
],
"uuid": "1abfb9bb-1a50-4a7f-aed6-cf1da70b0dfb"
}