{
"@context": "/terms/",
"@id": "/measurement-sets/IGVFDS2427TBFR/",
"@type": [
"MeasurementSet",
"FileSet",
"Item"
],
"accession": "IGVFDS2427TBFR",
"aliases": [
"jesse-engreitz:measurement_CRUDO_MYC-Auxin0hrs-FF2-BinC-PCR1_Rep1_S27",
"jesse-engreitz:measurement_CRUDO_MYC-Auxin0hrs-FF2-BinC-PCR1_Rep2_S82",
"jesse-engreitz:measurement_CRUDO_MYC-Auxin0hrs-FF2-BinC-PCR2_Rep1_S33",
"jesse-engreitz:measurement_CRUDO_MYC-Auxin0hrs-FF2-BinC-PCR2_Rep2_S88",
"jesse-engreitz:measurement_CRUDO_MYC-Auxin0hrs-FF2-BinC-PCR3_Rep1_S39",
"jesse-engreitz:measurement_CRUDO_MYC-Auxin0hrs-FF2-BinC-PCR3_Rep2_S94",
"jesse-engreitz:measurement_CRUDO_MYC-Auxin0hrs-FF2-BinC-PCR4_Rep1_S45",
"jesse-engreitz:measurement_CRUDO_MYC-Auxin0hrs-FF2-BinC-PCR4_Rep2_S100"
],
"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": "Measurement set [IGVFDS2427TBFR](/measurement-sets/IGVFDS2427TBFR/) 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/IGVFDS2427TBFR/"
},
{
"category": "missing sequencing kit",
"detail": "Measurement set [IGVFDS2427TBFR](/measurement-sets/IGVFDS2427TBFR/) has sequence file(s) [IGVFFI2767JLED](/sequence-files/IGVFFI2767JLED/), [IGVFFI8754LKYF](/sequence-files/IGVFFI8754LKYF/), [IGVFFI0106GQNO](/sequence-files/IGVFFI0106GQNO/), [IGVFFI9428EDUT](/sequence-files/IGVFFI9428EDUT/), [IGVFFI1435MZPM](/sequence-files/IGVFFI1435MZPM/), [IGVFFI3364QZVW](/sequence-files/IGVFFI3364QZVW/), [IGVFFI8510KORF](/sequence-files/IGVFFI8510KORF/), [IGVFFI4506XCFK](/sequence-files/IGVFFI4506XCFK/) 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/IGVFDS2427TBFR/"
},
{
"category": "missing publication",
"detail": "In vitro system [IGVFSM7258NLNH](/in-vitro-systems/IGVFSM7258NLNH/) 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/IGVFSM7258NLNH/"
},
{
"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 [IGVFSM7258NLNH](/in-vitro-systems/IGVFSM7258NLNH/) 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/IGVFSM7258NLNH/"
}
]
},
"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": [
{
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"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": "2024-05-21T17:16:11.243045+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": [
{
"@id": "/configuration-files/IGVFFI3205EXPI/",
"accession": "IGVFFI3205EXPI",
"aliases": [
"jesse-engreitz:seqspecfile_CRUDO_MYC-Auxin0hrs-FF2-BinC-PCR3_Rep2_S94"
],
"content_type": "seqspec",
"creation_timestamp": "2024-06-11T20:48:41.751425+00:00",
"file_format": "yaml",
"file_size": 911,
"href": "/configuration-files/IGVFFI3205EXPI/@@download/IGVFFI3205EXPI.yaml.gz",
"s3_uri": "s3://igvf-files/2024/06/11/05249149-ea1e-47f4-878b-03c8c5f9500b/IGVFFI3205EXPI.yaml.gz",
"status": "released",
"submitted_file_name": "/oak/stanford/groups/engreitz/Projects/Cohesin/240410_IGVF_upload/seqspec/guideseq.out.MYC-Auxin0hrs-FF2-BinC-PCR3_Rep2_S94.yaml",
"upload_status": "validation exempted"
},
{
"@id": "/configuration-files/IGVFFI6248PVCU/",
"accession": "IGVFFI6248PVCU",
"aliases": [
"jesse-engreitz:seqspecfile_CRUDO_MYC-Auxin0hrs-FF2-BinC-PCR1_Rep1_S27"
],
"content_type": "seqspec",
"creation_timestamp": "2024-06-11T20:47:30.041121+00:00",
"file_format": "yaml",
"file_size": 912,
"href": "/configuration-files/IGVFFI6248PVCU/@@download/IGVFFI6248PVCU.yaml.gz",
"s3_uri": "s3://igvf-files/2024/06/11/968dd58c-f807-4d91-8078-58acc46dd011/IGVFFI6248PVCU.yaml.gz",
"status": "released",
"submitted_file_name": "/oak/stanford/groups/engreitz/Projects/Cohesin/240410_IGVF_upload/seqspec/guideseq.out.MYC-Auxin0hrs-FF2-BinC-PCR1_Rep1_S27.yaml",
"upload_status": "validation exempted"
},
{
"@id": "/configuration-files/IGVFFI2776NKVA/",
"accession": "IGVFFI2776NKVA",
"aliases": [
"jesse-engreitz:seqspecfile_CRUDO_MYC-Auxin0hrs-FF2-BinC-PCR2_Rep1_S33"
],
"content_type": "seqspec",
"creation_timestamp": "2024-06-11T20:47:58.781757+00:00",
"file_format": "yaml",
"file_size": 910,
"href": "/configuration-files/IGVFFI2776NKVA/@@download/IGVFFI2776NKVA.yaml.gz",
"s3_uri": "s3://igvf-files/2024/06/11/c9628d26-bf4b-42a3-8f3e-51fb58f9aea1/IGVFFI2776NKVA.yaml.gz",
"status": "released",
"submitted_file_name": "/oak/stanford/groups/engreitz/Projects/Cohesin/240410_IGVF_upload/seqspec/guideseq.out.MYC-Auxin0hrs-FF2-BinC-PCR2_Rep1_S33.yaml",
"upload_status": "validation exempted"
},
{
"@id": "/configuration-files/IGVFFI2817XXHR/",
"accession": "IGVFFI2817XXHR",
"aliases": [
"jesse-engreitz:seqspecfile_CRUDO_MYC-Auxin0hrs-FF2-BinC-PCR1_Rep2_S82"
],
"content_type": "seqspec",
"creation_timestamp": "2024-06-11T20:47:44.504795+00:00",
"file_format": "yaml",
"file_size": 911,
"href": "/configuration-files/IGVFFI2817XXHR/@@download/IGVFFI2817XXHR.yaml.gz",
"s3_uri": "s3://igvf-files/2024/06/11/dceaf465-c28f-4650-b493-b52667a37ec7/IGVFFI2817XXHR.yaml.gz",
"status": "released",
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"upload_status": "validation exempted"
},
{
"@id": "/configuration-files/IGVFFI1384QEIW/",
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"aliases": [
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],
"content_type": "seqspec",
"creation_timestamp": "2024-06-11T20:48:56.125338+00:00",
"file_format": "yaml",
"file_size": 913,
"href": "/configuration-files/IGVFFI1384QEIW/@@download/IGVFFI1384QEIW.yaml.gz",
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"upload_status": "validation exempted"
},
{
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"accession": "IGVFFI2767JLED",
"aliases": [
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],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2024-06-01T02:02:18.529474+00:00",
"file_format": "fastq",
"file_size": 40728751,
"href": "/sequence-files/IGVFFI2767JLED/@@download/IGVFFI2767JLED.fastq.gz",
"s3_uri": "s3://igvf-files/2024/06/01/de63b1e0-7848-4138-80f3-892c8e98325f/IGVFFI2767JLED.fastq.gz",
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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-BinC-PCR3-Rep1_S39_R1_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/configuration-files/IGVFFI1879WVBZ/",
"accession": "IGVFFI1879WVBZ",
"aliases": [
"jesse-engreitz:seqspecfile_CRUDO_MYC-Auxin0hrs-FF2-BinC-PCR3_Rep1_S39"
],
"content_type": "seqspec",
"creation_timestamp": "2024-06-11T20:48:27.475324+00:00",
"file_format": "yaml",
"file_size": 911,
"href": "/configuration-files/IGVFFI1879WVBZ/@@download/IGVFFI1879WVBZ.yaml.gz",
"s3_uri": "s3://igvf-files/2024/06/11/25e28cfe-3bfe-4d96-bbfd-1af7cc3ca49e/IGVFFI1879WVBZ.yaml.gz",
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},
{
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"accession": "IGVFFI5550NXVT",
"aliases": [
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],
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"creation_timestamp": "2024-06-11T20:49:11.113263+00:00",
"file_format": "yaml",
"file_size": 913,
"href": "/configuration-files/IGVFFI5550NXVT/@@download/IGVFFI5550NXVT.yaml.gz",
"s3_uri": "s3://igvf-files/2024/06/11/8ddfbc70-1e4a-4afe-b6c0-057b0fa75928/IGVFFI5550NXVT.yaml.gz",
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"upload_status": "validation exempted"
},
{
"@id": "/configuration-files/IGVFFI1996ZSTC/",
"accession": "IGVFFI1996ZSTC",
"aliases": [
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],
"content_type": "seqspec",
"creation_timestamp": "2024-06-11T20:48:13.027376+00:00",
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"file_size": 910,
"href": "/configuration-files/IGVFFI1996ZSTC/@@download/IGVFFI1996ZSTC.yaml.gz",
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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-BinC-PCR1-Rep2_S82_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": "2024-07-10T19:47:07.762292+00:00",
"samples": [
{
"@id": "/in-vitro-systems/IGVFSM7258NLNH/",
"@type": [
"InVitroSystem",
"Biosample",
"Sample",
"Item"
],
"accession": "IGVFSM7258NLNH",
"aliases": [
"jesse-engreitz:in-vitro-system_CRUDO_MYC-Auxin0hrs-FF2-BinC-PCR1_Rep1_S27",
"jesse-engreitz:in-vitro-system_CRUDO_MYC-Auxin0hrs-FF2-BinC-PCR1_Rep2_S82",
"jesse-engreitz:in-vitro-system_CRUDO_MYC-Auxin0hrs-FF2-BinC-PCR2_Rep1_S33",
"jesse-engreitz:in-vitro-system_CRUDO_MYC-Auxin0hrs-FF2-BinC-PCR2_Rep2_S88",
"jesse-engreitz:in-vitro-system_CRUDO_MYC-Auxin0hrs-FF2-BinC-PCR3_Rep1_S39",
"jesse-engreitz:in-vitro-system_CRUDO_MYC-Auxin0hrs-FF2-BinC-PCR3_Rep2_S94",
"jesse-engreitz:in-vitro-system_CRUDO_MYC-Auxin0hrs-FF2-BinC-PCR4_Rep1_S45",
"jesse-engreitz:in-vitro-system_CRUDO_MYC-Auxin0hrs-FF2-BinC-PCR4_Rep2_S100"
],
"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 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": "2024-06-01T02:00:51.441233+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": "f34591f0-d4bc-4115-8b35-45edd98b7160"
}