{
"@context": "/terms/",
"@id": "/measurement-sets/IGVFDS3856ZADL/",
"@type": [
"MeasurementSet",
"FileSet",
"Item"
],
"accession": "IGVFDS3856ZADL",
"aliases": [
"jesse-engreitz:measurement_CRUDO_MYC-Auxin0hrs-FF2-BinA-PCR1_Rep1_S25",
"jesse-engreitz:measurement_CRUDO_MYC-Auxin0hrs-FF2-BinA-PCR1_Rep2_S80",
"jesse-engreitz:measurement_CRUDO_MYC-Auxin0hrs-FF2-BinA-PCR2_Rep1_S31",
"jesse-engreitz:measurement_CRUDO_MYC-Auxin0hrs-FF2-BinA-PCR2_Rep2_S86",
"jesse-engreitz:measurement_CRUDO_MYC-Auxin0hrs-FF2-BinA-PCR3_Rep1_S37",
"jesse-engreitz:measurement_CRUDO_MYC-Auxin0hrs-FF2-BinA-PCR3_Rep2_S92",
"jesse-engreitz:measurement_CRUDO_MYC-Auxin0hrs-FF2-BinA-PCR4_Rep1_S43",
"jesse-engreitz:measurement_CRUDO_MYC-Auxin0hrs-FF2-BinA-PCR4_Rep2_S98"
],
"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 [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/"
},
{
"category": "missing publication",
"detail": "Measurement set [IGVFDS3856ZADL](/measurement-sets/IGVFDS3856ZADL/) 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/IGVFDS3856ZADL/"
},
{
"category": "missing sequencing kit",
"detail": "Measurement set [IGVFDS3856ZADL](/measurement-sets/IGVFDS3856ZADL/) has sequence file(s) [IGVFFI0269PZHU](/sequence-files/IGVFFI0269PZHU/), [IGVFFI2787YXFO](/sequence-files/IGVFFI2787YXFO/), [IGVFFI3236SBJX](/sequence-files/IGVFFI3236SBJX/), [IGVFFI0450VGJL](/sequence-files/IGVFFI0450VGJL/), [IGVFFI6307WYZS](/sequence-files/IGVFFI6307WYZS/), [IGVFFI4364CKDK](/sequence-files/IGVFFI4364CKDK/), [IGVFFI3163PWLN](/sequence-files/IGVFFI3163PWLN/), [IGVFFI0700SJDG](/sequence-files/IGVFFI0700SJDG/) 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/IGVFDS3856ZADL/"
},
{
"category": "missing publication",
"detail": "In vitro system [IGVFSM6871QVFB](/in-vitro-systems/IGVFSM6871QVFB/) 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/IGVFSM6871QVFB/"
}
],
"WARNING": [
{
"category": "missing nucleic acid delivery",
"detail": "In vitro system [IGVFSM6871QVFB](/in-vitro-systems/IGVFSM6871QVFB/) 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/IGVFSM6871QVFB/"
}
]
},
"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"
},
"construct_library_sets": [
{
"@id": "/construct-library-sets/IGVFDS7857SYCK/",
"accession": "IGVFDS7857SYCK",
"file_set_type": "guide library",
"integrated_content_files": [
{
"@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": "2024-05-21T17:16:09.044789+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",
"files": [
{
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"accession": "IGVFFI7979CDQA",
"aliases": [
"jesse-engreitz:seqspecfile_CRUDO_MYC-Auxin0hrs-FF2-BinA-PCR4_Rep2_S98"
],
"content_type": "seqspec",
"creation_timestamp": "2024-06-11T20:49:06.175220+00:00",
"file_format": "yaml",
"file_size": 910,
"href": "/configuration-files/IGVFFI7979CDQA/@@download/IGVFFI7979CDQA.yaml.gz",
"s3_uri": "s3://igvf-files/2024/06/11/5cb64e80-f084-45fd-a858-9c1d2a3e4fe2/IGVFFI7979CDQA.yaml.gz",
"status": "released",
"submitted_file_name": "/oak/stanford/groups/engreitz/Projects/Cohesin/240410_IGVF_upload/seqspec/guideseq.out.MYC-Auxin0hrs-FF2-BinA-PCR4_Rep2_S98.yaml",
"upload_status": "validation exempted"
},
{
"@id": "/configuration-files/IGVFFI1710IDES/",
"accession": "IGVFFI1710IDES",
"aliases": [
"jesse-engreitz:seqspecfile_CRUDO_MYC-Auxin0hrs-FF2-BinA-PCR4_Rep1_S43"
],
"content_type": "seqspec",
"creation_timestamp": "2024-06-11T20:48:51.336011+00:00",
"file_format": "yaml",
"file_size": 910,
"href": "/configuration-files/IGVFFI1710IDES/@@download/IGVFFI1710IDES.yaml.gz",
"s3_uri": "s3://igvf-files/2024/06/11/d6ceceaf-7ec4-4412-8b7d-9c0dbb0a7dce/IGVFFI1710IDES.yaml.gz",
"status": "released",
"submitted_file_name": "/oak/stanford/groups/engreitz/Projects/Cohesin/240410_IGVF_upload/seqspec/guideseq.out.MYC-Auxin0hrs-FF2-BinA-PCR4_Rep1_S43.yaml",
"upload_status": "validation exempted"
},
{
"@id": "/configuration-files/IGVFFI8320WTKY/",
"accession": "IGVFFI8320WTKY",
"aliases": [
"jesse-engreitz:seqspecfile_CRUDO_MYC-Auxin0hrs-FF2-BinA-PCR1_Rep1_S25"
],
"content_type": "seqspec",
"creation_timestamp": "2024-06-11T20:47:25.114540+00:00",
"file_format": "yaml",
"file_size": 910,
"href": "/configuration-files/IGVFFI8320WTKY/@@download/IGVFFI8320WTKY.yaml.gz",
"s3_uri": "s3://igvf-files/2024/06/11/460c8fc2-6b65-4898-84fe-94b229fa9b97/IGVFFI8320WTKY.yaml.gz",
"status": "released",
"submitted_file_name": "/oak/stanford/groups/engreitz/Projects/Cohesin/240410_IGVF_upload/seqspec/guideseq.out.MYC-Auxin0hrs-FF2-BinA-PCR1_Rep1_S25.yaml",
"upload_status": "validation exempted"
},
{
"@id": "/configuration-files/IGVFFI4380QFIT/",
"accession": "IGVFFI4380QFIT",
"aliases": [
"jesse-engreitz:seqspecfile_CRUDO_MYC-Auxin0hrs-FF2-BinA-PCR1_Rep2_S80"
],
"content_type": "seqspec",
"creation_timestamp": "2024-06-11T20:47:39.745979+00:00",
"file_format": "yaml",
"file_size": 911,
"href": "/configuration-files/IGVFFI4380QFIT/@@download/IGVFFI4380QFIT.yaml.gz",
"s3_uri": "s3://igvf-files/2024/06/11/8e858a1e-6440-41e3-91b1-4ef0f8e6aa3a/IGVFFI4380QFIT.yaml.gz",
"status": "released",
"submitted_file_name": "/oak/stanford/groups/engreitz/Projects/Cohesin/240410_IGVF_upload/seqspec/guideseq.out.MYC-Auxin0hrs-FF2-BinA-PCR1_Rep2_S80.yaml",
"upload_status": "validation exempted"
},
{
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"accession": "IGVFFI9283MPSI",
"aliases": [
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],
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"creation_timestamp": "2024-06-11T20:48:08.421040+00:00",
"file_format": "yaml",
"file_size": 912,
"href": "/configuration-files/IGVFFI9283MPSI/@@download/IGVFFI9283MPSI.yaml.gz",
"s3_uri": "s3://igvf-files/2024/06/11/9cef3a7f-1d2c-4d3b-a0d6-59756f63c8ab/IGVFFI9283MPSI.yaml.gz",
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"upload_status": "validation exempted"
},
{
"@id": "/sequence-files/IGVFFI0269PZHU/",
"accession": "IGVFFI0269PZHU",
"aliases": [
"jesse-engreitz:auxiliary_file_CRUDO_MYC-Auxin0hrs-FF2-BinA-PCR3_Rep1_S37"
],
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"controlled_access": false,
"creation_timestamp": "2024-06-01T02:02:11.613420+00:00",
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"file_size": 41754604,
"href": "/sequence-files/IGVFFI0269PZHU/@@download/IGVFFI0269PZHU.fastq.gz",
"s3_uri": "s3://igvf-files/2024/06/01/c620f2c2-a807-4315-b41f-071c9149963b/IGVFFI0269PZHU.fastq.gz",
"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-BinA-PCR3-Rep1_S37_R1_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/configuration-files/IGVFFI6808FPSN/",
"accession": "IGVFFI6808FPSN",
"aliases": [
"jesse-engreitz:seqspecfile_CRUDO_MYC-Auxin0hrs-FF2-BinA-PCR2_Rep1_S31"
],
"content_type": "seqspec",
"creation_timestamp": "2024-06-11T20:47:54.180610+00:00",
"file_format": "yaml",
"file_size": 912,
"href": "/configuration-files/IGVFFI6808FPSN/@@download/IGVFFI6808FPSN.yaml.gz",
"s3_uri": "s3://igvf-files/2024/06/11/0da87408-111a-4209-b58d-4bc9805d8556/IGVFFI6808FPSN.yaml.gz",
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"upload_status": "validation exempted"
},
{
"@id": "/configuration-files/IGVFFI3170BIJY/",
"accession": "IGVFFI3170BIJY",
"aliases": [
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],
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"href": "/configuration-files/IGVFFI3170BIJY/@@download/IGVFFI3170BIJY.yaml.gz",
"s3_uri": "s3://igvf-files/2024/06/11/197ab0dc-d542-4e06-ab3b-ce9985d9f008/IGVFFI3170BIJY.yaml.gz",
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"submitted_file_name": "/oak/stanford/groups/engreitz/Projects/Cohesin/240410_IGVF_upload/seqspec/guideseq.out.MYC-Auxin0hrs-FF2-BinA-PCR3_Rep2_S92.yaml",
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},
{
"@id": "/configuration-files/IGVFFI1697OBKN/",
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],
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"href": "/configuration-files/IGVFFI1697OBKN/@@download/IGVFFI1697OBKN.yaml.gz",
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},
{
"@id": "/sequence-files/IGVFFI2787YXFO/",
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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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},
{
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},
"status": "released",
"submitted_file_name": "/oak/stanford/groups/engreitz/Projects/Cohesin/220819B015_MYC/fastq_trim/MYC-Auxin0hrs-FF2-BinA-PCR4-Rep1_S43_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": "2024-07-10T19:46:52.932787+00:00",
"samples": [
{
"@id": "/in-vitro-systems/IGVFSM6871QVFB/",
"@type": [
"InVitroSystem",
"Biosample",
"Sample",
"Item"
],
"accession": "IGVFSM6871QVFB",
"aliases": [
"jesse-engreitz:in-vitro-system_CRUDO_MYC-Auxin0hrs-FF2-BinA-PCR1_Rep1_S25",
"jesse-engreitz:in-vitro-system_CRUDO_MYC-Auxin0hrs-FF2-BinA-PCR1_Rep2_S80",
"jesse-engreitz:in-vitro-system_CRUDO_MYC-Auxin0hrs-FF2-BinA-PCR2_Rep1_S31",
"jesse-engreitz:in-vitro-system_CRUDO_MYC-Auxin0hrs-FF2-BinA-PCR2_Rep2_S86",
"jesse-engreitz:in-vitro-system_CRUDO_MYC-Auxin0hrs-FF2-BinA-PCR3_Rep1_S37",
"jesse-engreitz:in-vitro-system_CRUDO_MYC-Auxin0hrs-FF2-BinA-PCR3_Rep2_S92",
"jesse-engreitz:in-vitro-system_CRUDO_MYC-Auxin0hrs-FF2-BinA-PCR4_Rep1_S43",
"jesse-engreitz:in-vitro-system_CRUDO_MYC-Auxin0hrs-FF2-BinA-PCR4_Rep2_S98"
],
"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 A for 0-10% 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": "2024-06-01T02:00:44.627135+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": "529784b6-5657-41a5-b248-d4356b91cf0c"
}