{
"@context": "/terms/",
"@id": "/measurement-sets/IGVFDS7409OQIL/",
"@type": [
"MeasurementSet",
"FileSet",
"Item"
],
"accession": "IGVFDS7409OQIL",
"aliases": [
"jesse-engreitz:measurement_CRUDO_MYC-Auxin0hrs-FF1-BinD-PCR1_Rep1_S4",
"jesse-engreitz:measurement_CRUDO_MYC-Auxin0hrs-FF1-BinD-PCR1_Rep2_S59",
"jesse-engreitz:measurement_CRUDO_MYC-Auxin0hrs-FF1-BinD-PCR2_Rep1_S10",
"jesse-engreitz:measurement_CRUDO_MYC-Auxin0hrs-FF1-BinD-PCR2_Rep2_S65",
"jesse-engreitz:measurement_CRUDO_MYC-Auxin0hrs-FF1-BinD-PCR3_Rep1_S16",
"jesse-engreitz:measurement_CRUDO_MYC-Auxin0hrs-FF1-BinD-PCR3_Rep2_S71",
"jesse-engreitz:measurement_CRUDO_MYC-Auxin0hrs-FF1-BinD-PCR4_Rep1_S22",
"jesse-engreitz:measurement_CRUDO_MYC-Auxin0hrs-FF1-BinD-PCR4_Rep2_S77"
],
"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": "Auxiliary set [IGVFDS5951VSHM](/auxiliary-sets/IGVFDS5951VSHM/) 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/IGVFDS5951VSHM/"
},
{
"category": "missing publication",
"detail": "Measurement set [IGVFDS7409OQIL](/measurement-sets/IGVFDS7409OQIL/) 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/IGVFDS7409OQIL/"
},
{
"category": "missing sequencing kit",
"detail": "Measurement set [IGVFDS7409OQIL](/measurement-sets/IGVFDS7409OQIL/) has sequence file(s) [IGVFFI2143VXMF](/sequence-files/IGVFFI2143VXMF/), [IGVFFI4680QVWM](/sequence-files/IGVFFI4680QVWM/), [IGVFFI9320EENZ](/sequence-files/IGVFFI9320EENZ/), [IGVFFI0342EICI](/sequence-files/IGVFFI0342EICI/), [IGVFFI3107NMCV](/sequence-files/IGVFFI3107NMCV/), [IGVFFI6727EKGM](/sequence-files/IGVFFI6727EKGM/), [IGVFFI3177EXCB](/sequence-files/IGVFFI3177EXCB/), [IGVFFI8552NKOB](/sequence-files/IGVFFI8552NKOB/) 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/IGVFDS7409OQIL/"
},
{
"category": "missing publication",
"detail": "In vitro system [IGVFSM0111NTPA](/in-vitro-systems/IGVFSM0111NTPA/) 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/IGVFSM0111NTPA/"
}
],
"WARNING": [
{
"category": "missing nucleic acid delivery",
"detail": "In vitro system [IGVFSM0111NTPA](/in-vitro-systems/IGVFSM0111NTPA/) 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/IGVFSM0111NTPA/"
}
]
},
"auxiliary_sets": [
{
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"accession": "IGVFDS5951VSHM",
"aliases": [
"jesse-engreitz:auxiliary_sortparams_CRUDO_MYC-Auxin0hrs-FF1"
],
"file_set_type": "cell sorting",
"status": "released"
}
],
"award": {
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"component": "functional characterization",
"contact_pi": {
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"title": "Jesse Engreitz"
},
"title": "Stanford Center for Connecting DNA Variants to Function and Phenotype"
},
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{
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"accession": "IGVFDS7857SYCK",
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{
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"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": "2024-05-21T17:15:17.256009+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",
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{
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"accession": "IGVFFI5922AKJR",
"aliases": [
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],
"content_type": "seqspec",
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"file_format": "yaml",
"file_size": 910,
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"md5sum": "07566c4bdb82a73bea0eb9f6e82b7758",
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"upload_status": "validation exempted"
},
{
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"accession": "IGVFFI6755HBWI",
"aliases": [
"jesse-engreitz:seqspecfile_CRUDO_MYC-Auxin0hrs-FF1-BinD-PCR3_Rep2_S71"
],
"content_type": "seqspec",
"creation_timestamp": "2024-06-11T20:46:49.843394+00:00",
"file_format": "yaml",
"file_size": 910,
"href": "/configuration-files/IGVFFI6755HBWI/@@download/IGVFFI6755HBWI.yaml.gz",
"md5sum": "198555d74d1eefda2669f382a45c1c5f",
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"status": "released",
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"upload_status": "validation exempted"
},
{
"@id": "/configuration-files/IGVFFI5598HNTC/",
"accession": "IGVFFI5598HNTC",
"aliases": [
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],
"content_type": "seqspec",
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"file_format": "yaml",
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"href": "/configuration-files/IGVFFI5598HNTC/@@download/IGVFFI5598HNTC.yaml.gz",
"md5sum": "b8e3c6ad7a4e5c7c925f0c8fefed0b95",
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"status": "released",
"submitted_file_name": "/oak/stanford/groups/engreitz/Projects/Cohesin/240410_IGVF_upload/seqspec/guideseq.out.MYC-Auxin0hrs-FF1-BinD-PCR2_Rep1_S10.yaml",
"upload_status": "validation exempted"
},
{
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"accession": "IGVFFI0808YUDW",
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],
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"creation_timestamp": "2024-06-11T20:45:54.049564+00:00",
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},
{
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],
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},
{
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],
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"md5sum": "3c34233d27177fe8ae3d5f2a17190cc7",
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"term_name": "Illumina HiSeq 2500"
},
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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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},
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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-FF1-BinD-PCR4-Rep2_S77_R1_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI8552NKOB/",
"accession": "IGVFFI8552NKOB",
"aliases": [
"jesse-engreitz:auxiliary_file_CRUDO_MYC-Auxin0hrs-FF1-BinD-PCR2_Rep2_S65"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2024-06-01T01:59:12.982173+00:00",
"file_format": "fastq",
"file_size": 28701240,
"href": "/sequence-files/IGVFFI8552NKOB/@@download/IGVFFI8552NKOB.fastq.gz",
"md5sum": "cff17ab7317ed49b39d86c5fbd22ce58",
"s3_uri": "s3://igvf-files/2024/06/01/da39e7a4-f793-41a3-a510-adf485077fc1/IGVFFI8552NKOB.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/220819B015_MYC/fastq_trim/MYC-Auxin0hrs-FF1-BinD-PCR2-Rep2_S65_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": "2024-07-10T19:46:33.636929+00:00",
"samples": [
{
"@id": "/in-vitro-systems/IGVFSM0111NTPA/",
"@type": [
"InVitroSystem",
"Biosample",
"Sample",
"Item"
],
"accession": "IGVFSM0111NTPA",
"aliases": [
"jesse-engreitz:in-vitro-system_CRUDO_MYC-Auxin0hrs-FF1-BinD-PCR1_Rep1_S4",
"jesse-engreitz:in-vitro-system_CRUDO_MYC-Auxin0hrs-FF1-BinD-PCR1_Rep2_S59",
"jesse-engreitz:in-vitro-system_CRUDO_MYC-Auxin0hrs-FF1-BinD-PCR2_Rep1_S10",
"jesse-engreitz:in-vitro-system_CRUDO_MYC-Auxin0hrs-FF1-BinD-PCR2_Rep2_S65",
"jesse-engreitz:in-vitro-system_CRUDO_MYC-Auxin0hrs-FF1-BinD-PCR3_Rep1_S16",
"jesse-engreitz:in-vitro-system_CRUDO_MYC-Auxin0hrs-FF1-BinD-PCR3_Rep2_S71",
"jesse-engreitz:in-vitro-system_CRUDO_MYC-Auxin0hrs-FF1-BinD-PCR4_Rep1_S22",
"jesse-engreitz:in-vitro-system_CRUDO_MYC-Auxin0hrs-FF1-BinD-PCR4_Rep2_S77"
],
"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 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": "2024-06-01T01:58:10.657499+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": "0260cb2d-aec2-498e-aef0-12c6ac7b9abd"
}