{
"@context": "/terms/",
"@id": "/construct-library-sets/IGVFDS9869EMNE/",
"@type": [
"ConstructLibrarySet",
"FileSet",
"Item"
],
"accession": "IGVFDS9869EMNE",
"aliases": [
"jesse-engreitz:construct_library_CRUDO_TAPseq"
],
"applied_to_samples": [
{
"@id": "/in-vitro-systems/IGVFSM9983LVUX/",
"@type": [
"InVitroSystem",
"Biosample",
"Sample",
"Item"
],
"accession": "IGVFSM9983LVUX",
"aliases": [
"jesse-engreitz:in-vitro-system_CRUDO_TAPseq-Auxin6hrs-Rep1"
],
"classifications": [
"cell line"
],
"donors": [
{
"@id": "/human-donors/IGVFDO0384OZRW/",
"taxa": "Homo sapiens"
}
],
"modifications": [
{
"@id": "/degron-modifications/95081d1b-08b4-49ed-b324-e53fc43d8456/",
"modality": "degradation",
"summary": "AID system targeting RAD21"
},
{
"@id": "/crispr-modifications/8543fa06-1720-4e7d-8e8f-7e24c1b1cf79/",
"modality": "interference",
"summary": "CRISPRi Sp-dCas9-KOX1-KRAB"
}
],
"sample_terms": [
{
"@id": "/sample-terms/EFO_0002824/",
"term_name": "HCT116"
}
],
"status": "released",
"summary": "HCT116 cell line, male, Homo sapiens treated with 1 μM 5-Phenyl-1H-indole-3-acetic acid for 6 hours, modified with AID system targeting RAD21, CRISPRi Sp-dCas9-KOX1-KRAB, transfected with a guide library",
"treatments": [
{
"@id": "/treatments/d35868d1-c45b-49ae-8ff3-a9c0c22551c2/",
"summary": "Treatment of 1 μM 5-Phenyl-1H-indole-3-acetic acid for 6 hours",
"treatment_term_name": "5-Phenyl-1H-indole-3-acetic acid"
}
]
},
{
"@id": "/in-vitro-systems/IGVFSM2061VHMZ/",
"@type": [
"InVitroSystem",
"Biosample",
"Sample",
"Item"
],
"accession": "IGVFSM2061VHMZ",
"aliases": [
"jesse-engreitz:in-vitro-system_CRUDO_TAPseq-Rep2"
],
"classifications": [
"cell line"
],
"donors": [
{
"@id": "/human-donors/IGVFDO0384OZRW/",
"taxa": "Homo sapiens"
}
],
"modifications": [
{
"@id": "/degron-modifications/2e8d10cc-fc98-44d5-a7d9-e2892e16c98a/",
"modality": "degradation",
"summary": "inactive AID system targeting RAD21"
},
{
"@id": "/crispr-modifications/8543fa06-1720-4e7d-8e8f-7e24c1b1cf79/",
"modality": "interference",
"summary": "CRISPRi Sp-dCas9-KOX1-KRAB"
}
],
"sample_terms": [
{
"@id": "/sample-terms/EFO_0002824/",
"term_name": "HCT116"
}
],
"status": "released",
"summary": "HCT116 cell line, male, Homo sapiens modified with CRISPRi Sp-dCas9-KOX1-KRAB, inactive AID system targeting RAD21, transfected with a guide library"
},
{
"@id": "/in-vitro-systems/IGVFSM5799ZEJH/",
"@type": [
"InVitroSystem",
"Biosample",
"Sample",
"Item"
],
"accession": "IGVFSM5799ZEJH",
"aliases": [
"jesse-engreitz:in-vitro-system_CRUDO_TAPseq-Auxin0hrs-Rep1"
],
"classifications": [
"cell line"
],
"donors": [
{
"@id": "/human-donors/IGVFDO0384OZRW/",
"taxa": "Homo sapiens"
}
],
"modifications": [
{
"@id": "/crispr-modifications/8543fa06-1720-4e7d-8e8f-7e24c1b1cf79/",
"modality": "interference",
"summary": "CRISPRi Sp-dCas9-KOX1-KRAB"
},
{
"@id": "/degron-modifications/2e8d10cc-fc98-44d5-a7d9-e2892e16c98a/",
"modality": "degradation",
"summary": "inactive AID system targeting RAD21"
}
],
"sample_terms": [
{
"@id": "/sample-terms/EFO_0002824/",
"term_name": "HCT116"
}
],
"status": "released",
"summary": "HCT116 cell line, male, Homo sapiens modified with CRISPRi Sp-dCas9-KOX1-KRAB, inactive AID system targeting RAD21, transfected with a guide library"
},
{
"@id": "/in-vitro-systems/IGVFSM0767GJUV/",
"@type": [
"InVitroSystem",
"Biosample",
"Sample",
"Item"
],
"accession": "IGVFSM0767GJUV",
"aliases": [
"jesse-engreitz:in-vitro-system_CRUDO_TAPseq-Auxin0hrs-Rep2"
],
"classifications": [
"cell line"
],
"donors": [
{
"@id": "/human-donors/IGVFDO0384OZRW/",
"taxa": "Homo sapiens"
}
],
"modifications": [
{
"@id": "/crispr-modifications/8543fa06-1720-4e7d-8e8f-7e24c1b1cf79/",
"modality": "interference",
"summary": "CRISPRi Sp-dCas9-KOX1-KRAB"
},
{
"@id": "/degron-modifications/2e8d10cc-fc98-44d5-a7d9-e2892e16c98a/",
"modality": "degradation",
"summary": "inactive AID system targeting RAD21"
}
],
"sample_terms": [
{
"@id": "/sample-terms/EFO_0002824/",
"term_name": "HCT116"
}
],
"status": "released",
"summary": "HCT116 cell line, male, Homo sapiens modified with CRISPRi Sp-dCas9-KOX1-KRAB, inactive AID system targeting RAD21, transfected with a guide library"
},
{
"@id": "/in-vitro-systems/IGVFSM8511JOMW/",
"@type": [
"InVitroSystem",
"Biosample",
"Sample",
"Item"
],
"accession": "IGVFSM8511JOMW",
"aliases": [
"jesse-engreitz:in-vitro-system_CRUDO_TAPseq-Auxin6hrs-Rep2"
],
"classifications": [
"cell line"
],
"donors": [
{
"@id": "/human-donors/IGVFDO0384OZRW/",
"taxa": "Homo sapiens"
}
],
"modifications": [
{
"@id": "/degron-modifications/95081d1b-08b4-49ed-b324-e53fc43d8456/",
"modality": "degradation",
"summary": "AID system targeting RAD21"
},
{
"@id": "/crispr-modifications/8543fa06-1720-4e7d-8e8f-7e24c1b1cf79/",
"modality": "interference",
"summary": "CRISPRi Sp-dCas9-KOX1-KRAB"
}
],
"sample_terms": [
{
"@id": "/sample-terms/EFO_0002824/",
"term_name": "HCT116"
}
],
"status": "released",
"summary": "HCT116 cell line, male, Homo sapiens treated with 1 μM 5-Phenyl-1H-indole-3-acetic acid for 6 hours, modified with AID system targeting RAD21, CRISPRi Sp-dCas9-KOX1-KRAB, transfected with a guide library",
"treatments": [
{
"@id": "/treatments/d35868d1-c45b-49ae-8ff3-a9c0c22551c2/",
"summary": "Treatment of 1 μM 5-Phenyl-1H-indole-3-acetic acid for 6 hours",
"treatment_term_name": "5-Phenyl-1H-indole-3-acetic acid"
}
]
},
{
"@id": "/in-vitro-systems/IGVFSM5760JFFX/",
"@type": [
"InVitroSystem",
"Biosample",
"Sample",
"Item"
],
"accession": "IGVFSM5760JFFX",
"aliases": [
"jesse-engreitz:in-vitro-system_CRUDO_TAPseq-Rep1"
],
"classifications": [
"cell line"
],
"donors": [
{
"@id": "/human-donors/IGVFDO0384OZRW/",
"taxa": "Homo sapiens"
}
],
"modifications": [
{
"@id": "/degron-modifications/2e8d10cc-fc98-44d5-a7d9-e2892e16c98a/",
"modality": "degradation",
"summary": "inactive AID system targeting RAD21"
},
{
"@id": "/crispr-modifications/8543fa06-1720-4e7d-8e8f-7e24c1b1cf79/",
"modality": "interference",
"summary": "CRISPRi Sp-dCas9-KOX1-KRAB"
}
],
"sample_terms": [
{
"@id": "/sample-terms/EFO_0002824/",
"term_name": "HCT116"
}
],
"status": "released",
"summary": "HCT116 cell line, male, Homo sapiens modified with CRISPRi Sp-dCas9-KOX1-KRAB, inactive AID system targeting RAD21, transfected with a guide library"
}
],
"audit": {
"NOT_COMPLIANT": [
{
"category": "missing sequencing kit",
"detail": "Construct library set [IGVFDS9869EMNE](/construct-library-sets/IGVFDS9869EMNE/) has sequence file(s) [IGVFFI7017ICQL](/sequence-files/IGVFFI7017ICQL/) which lack specification of a `sequencing_kit`. Sequence files should specify a sequencing kit.",
"level": 50,
"level_name": "NOT_COMPLIANT",
"name": "audit_inconsistent_sequencing_kit",
"path": "/construct-library-sets/IGVFDS9869EMNE/"
}
],
"WARNING": [
{
"category": "missing analysis",
"detail": "Construct library set [IGVFDS9869EMNE](/construct-library-sets/IGVFDS9869EMNE/) is a raw data set with files, but is not listed in any `input_file_sets` for any analysis sets. Raw data sets with files are expected to be associated with at least one analysis set.",
"level": 40,
"level_name": "WARNING",
"name": "audit_input_for",
"path": "/construct-library-sets/IGVFDS9869EMNE/"
}
]
},
"award": {
"@id": "/awards/HG011972/",
"component": "functional characterization"
},
"control_for": [],
"creation_timestamp": "2024-06-06T17:55:14.122190+00:00",
"documents": [
"/documents/6f05cff9-a97a-45f7-9503-ebd5c44873b0/"
],
"file_set_type": "guide library",
"files": [
{
"@id": "/sequence-files/IGVFFI7017ICQL/",
"accession": "IGVFFI7017ICQL",
"aliases": [
"jesse-engreitz:gRNAlibrary_file_CRUDO_TAPseq"
],
"content_type": "reads",
"file_format": "fastq",
"upload_status": "validated"
},
{
"@id": "/configuration-files/IGVFFI0944DQUA/",
"accession": "IGVFFI0944DQUA",
"aliases": [
"jesse-engreitz:seqspecfile_testguideseq_CRUDO_TAPseq"
],
"content_type": "seqspec",
"file_format": "yaml",
"upload_status": "validated"
}
],
"guide_type": "sgRNA",
"input_for": [],
"integrated_content_files": [
{
"@id": "/tabular-files/IGVFFI5298NREB/",
"accession": "IGVFFI5298NREB",
"aliases": [
"jesse-engreitz:guidedesign_file_CRUDO_TAPseq"
],
"content_type": "guide RNA sequences",
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"upload_status": "validated"
}
],
"lab": {
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"title": "Jesse Engreitz, Stanford"
},
"release_timestamp": "2024-07-10T19:53:27.817316+00:00",
"schema_version": "10",
"scope": "loci",
"selection_criteria": [
"accessible genome regions"
],
"small_scale_loci_list": [
{
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"start": 69352659
},
{
"assembly": "GRCh38",
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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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{
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{
"assembly": "GRCh38",
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},
{
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{
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{
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{
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},
{
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}
],
"sources": [
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],
"status": "released",
"submitted_by": {
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"title": "Benjamin Doughty"
},
"submitted_files_timestamp": "2024-06-06T17:55:54.696319+00:00",
"summary": "Guide (sgRNA) library targeting accessible genome regions in 29 genomic loci",
"tiling_modality": "sparse peaks",
"uuid": "64a6d5d9-f026-4aab-ba29-dea1672a0065"
}