{
"@context": "/terms/",
"@id": "/construct-library-sets/IGVFDS0392OWNZ/",
"@type": [
"ConstructLibrarySet",
"FileSet",
"Item"
],
"accession": "IGVFDS0392OWNZ",
"aliases": [
"jesse-engreitz:construct_library_CRUDO_PILOT_CCND1"
],
"applied_to_samples": [
{
"@id": "/in-vitro-systems/IGVFSM1436SJKL/",
"@type": [
"InVitroSystem",
"Biosample",
"Sample",
"Item"
],
"accession": "IGVFSM1436SJKL",
"aliases": [
"jesse-engreitz:in-vitro-system_CRUDO_PILOT"
],
"classifications": [
"cell line"
],
"donors": [
{
"@id": "/human-donors/IGVFDO0384OZRW/",
"taxa": "Homo sapiens"
}
],
"sample_terms": [
{
"@id": "/sample-terms/EFO_0002824/",
"term_name": "HCT116"
}
],
"status": "released",
"summary": "HCT116 cell line, male, Homo sapiens modified with a guide library"
},
{
"@id": "/in-vitro-systems/IGVFSM9116DXLY/",
"@type": [
"InVitroSystem",
"Biosample",
"Sample",
"Item"
],
"accession": "IGVFSM9116DXLY",
"aliases": [
"jesse-engreitz:in-vitro-system_CRUDO_PILOT_CCND1-Auxin6hrs-FF1-BinE-PCR1_S5",
"jesse-engreitz:in-vitro-system_CRUDO_PILOT_CCND1-Auxin6hrs-FF1-BinE-PCR2_S101",
"jesse-engreitz:in-vitro-system_CRUDO_PILOT_CCND1-Auxin6hrs-FF1-BinE-PCR3_S197",
"jesse-engreitz:in-vitro-system_CRUDO_PILOT_CCND1-Auxin6hrs-FF1-BinE-PCR4_S293"
],
"classifications": [
"cell line"
],
"donors": [
{
"@id": "/human-donors/IGVFDO0384OZRW/",
"taxa": "Homo sapiens"
}
],
"sample_terms": [
{
"@id": "/sample-terms/EFO_0002824/",
"term_name": "HCT116"
}
],
"status": "released",
"summary": "HCT116 cell line, male, Homo sapiens (sorting details: FACS bin E for 80-90% expression of CCND1) treated with 1 μM 5-Phenyl-1H-indole-3-acetic acid for 6 hours, modified with a guide library"
},
{
"@id": "/in-vitro-systems/IGVFSM5079ZTJX/",
"@type": [
"InVitroSystem",
"Biosample",
"Sample",
"Item"
],
"accession": "IGVFSM5079ZTJX",
"aliases": [
"jesse-engreitz:in-vitro-system_CRUDO_PILOT_CCND1-Auxin0hrs-FF1-BinC-PCR1_S75",
"jesse-engreitz:in-vitro-system_CRUDO_PILOT_CCND1-Auxin0hrs-FF1-BinC-PCR2_S171",
"jesse-engreitz:in-vitro-system_CRUDO_PILOT_CCND1-Auxin0hrs-FF1-BinC-PCR3_S267",
"jesse-engreitz:in-vitro-system_CRUDO_PILOT_CCND1-Auxin0hrs-FF1-BinC-PCR4_S363"
],
"classifications": [
"cell line"
],
"donors": [
{
"@id": "/human-donors/IGVFDO0384OZRW/",
"taxa": "Homo sapiens"
}
],
"sample_terms": [
{
"@id": "/sample-terms/EFO_0002824/",
"term_name": "HCT116"
}
],
"status": "released",
"summary": "HCT116 cell line, male, Homo sapiens (sorting details: FACS bin C for 35-45% expression of CCND1) modified with a guide library"
},
{
"@id": "/in-vitro-systems/IGVFSM7865RIGH/",
"@type": [
"InVitroSystem",
"Biosample",
"Sample",
"Item"
],
"accession": "IGVFSM7865RIGH",
"aliases": [
"jesse-engreitz:in-vitro-system_CRUDO_PILOT_CCND1-Auxin0hrs-FF1-BinA-PCR1_S73",
"jesse-engreitz:in-vitro-system_CRUDO_PILOT_CCND1-Auxin0hrs-FF1-BinA-PCR2_S169",
"jesse-engreitz:in-vitro-system_CRUDO_PILOT_CCND1-Auxin0hrs-FF1-BinA-PCR3_S265",
"jesse-engreitz:in-vitro-system_CRUDO_PILOT_CCND1-Auxin0hrs-FF1-BinA-PCR4_S361"
],
"classifications": [
"cell line"
],
"donors": [
{
"@id": "/human-donors/IGVFDO0384OZRW/",
"taxa": "Homo sapiens"
}
],
"sample_terms": [
{
"@id": "/sample-terms/EFO_0002824/",
"term_name": "HCT116"
}
],
"status": "released",
"summary": "HCT116 cell line, male, Homo sapiens (sorting details: FACS bin A for 0-10% expression of CCND1) modified with a guide library"
},
{
"@id": "/in-vitro-systems/IGVFSM0904FNLS/",
"@type": [
"InVitroSystem",
"Biosample",
"Sample",
"Item"
],
"accession": "IGVFSM0904FNLS",
"aliases": [
"jesse-engreitz:in-vitro-system_CRUDO_PILOT_CCND1-Auxin6hrs-FF1-BinF-PCR1_S6",
"jesse-engreitz:in-vitro-system_CRUDO_PILOT_CCND1-Auxin6hrs-FF1-BinF-PCR2_S102",
"jesse-engreitz:in-vitro-system_CRUDO_PILOT_CCND1-Auxin6hrs-FF1-BinF-PCR3_S198",
"jesse-engreitz:in-vitro-system_CRUDO_PILOT_CCND1-Auxin6hrs-FF1-BinF-PCR4_S294"
],
"classifications": [
"cell line"
],
"donors": [
{
"@id": "/human-donors/IGVFDO0384OZRW/",
"taxa": "Homo sapiens"
}
],
"sample_terms": [
{
"@id": "/sample-terms/EFO_0002824/",
"term_name": "HCT116"
}
],
"status": "released",
"summary": "HCT116 cell line, male, Homo sapiens (sorting details: FACS bin F for 80-100% expression of CCND1) treated with 1 μM 5-Phenyl-1H-indole-3-acetic acid for 6 hours, modified with a guide library"
},
{
"@id": "/in-vitro-systems/IGVFSM6480FETB/",
"@type": [
"InVitroSystem",
"Biosample",
"Sample",
"Item"
],
"accession": "IGVFSM6480FETB",
"aliases": [
"jesse-engreitz:in-vitro-system_CRUDO_PILOT_CCND1-Auxin6hrs-FF1-BinC-PCR1_S3",
"jesse-engreitz:in-vitro-system_CRUDO_PILOT_CCND1-Auxin6hrs-FF1-BinC-PCR2_S99",
"jesse-engreitz:in-vitro-system_CRUDO_PILOT_CCND1-Auxin6hrs-FF1-BinC-PCR3_S195",
"jesse-engreitz:in-vitro-system_CRUDO_PILOT_CCND1-Auxin6hrs-FF1-BinC-PCR4_S291"
],
"classifications": [
"cell line"
],
"donors": [
{
"@id": "/human-donors/IGVFDO0384OZRW/",
"taxa": "Homo sapiens"
}
],
"sample_terms": [
{
"@id": "/sample-terms/EFO_0002824/",
"term_name": "HCT116"
}
],
"status": "released",
"summary": "HCT116 cell line, male, Homo sapiens (sorting details: FACS bin C for 35-45% expression of CCND1) treated with 1 μM 5-Phenyl-1H-indole-3-acetic acid for 6 hours, modified with a guide library"
},
{
"@id": "/in-vitro-systems/IGVFSM6219XAXK/",
"@type": [
"InVitroSystem",
"Biosample",
"Sample",
"Item"
],
"accession": "IGVFSM6219XAXK",
"aliases": [
"jesse-engreitz:in-vitro-system_CRUDO_PILOT_Auxin6hrs"
],
"classifications": [
"cell line"
],
"donors": [
{
"@id": "/human-donors/IGVFDO0384OZRW/",
"taxa": "Homo sapiens"
}
],
"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 a guide library"
},
{
"@id": "/in-vitro-systems/IGVFSM3580KDPA/",
"@type": [
"InVitroSystem",
"Biosample",
"Sample",
"Item"
],
"accession": "IGVFSM3580KDPA",
"aliases": [
"jesse-engreitz:in-vitro-system_CRUDO_PILOT_Auxin0hrs"
],
"classifications": [
"cell line"
],
"donors": [
{
"@id": "/human-donors/IGVFDO0384OZRW/",
"taxa": "Homo sapiens"
}
],
"sample_terms": [
{
"@id": "/sample-terms/EFO_0002824/",
"term_name": "HCT116"
}
],
"status": "released",
"summary": "HCT116 cell line, male, Homo sapiens modified with a guide library"
},
{
"@id": "/in-vitro-systems/IGVFSM1617PVUY/",
"@type": [
"InVitroSystem",
"Biosample",
"Sample",
"Item"
],
"accession": "IGVFSM1617PVUY",
"aliases": [
"jesse-engreitz:in-vitro-system_CRUDO_PILOT_CCND1-Auxin0hrs-FF1-BinE-PCR1_S77",
"jesse-engreitz:in-vitro-system_CRUDO_PILOT_CCND1-Auxin0hrs-FF1-BinE-PCR2_S173",
"jesse-engreitz:in-vitro-system_CRUDO_PILOT_CCND1-Auxin0hrs-FF1-BinE-PCR3_S269",
"jesse-engreitz:in-vitro-system_CRUDO_PILOT_CCND1-Auxin0hrs-FF1-BinE-PCR4_S365"
],
"classifications": [
"cell line"
],
"donors": [
{
"@id": "/human-donors/IGVFDO0384OZRW/",
"taxa": "Homo sapiens"
}
],
"sample_terms": [
{
"@id": "/sample-terms/EFO_0002824/",
"term_name": "HCT116"
}
],
"status": "released",
"summary": "HCT116 cell line, male, Homo sapiens (sorting details: FACS bin E for 80-90% expression of CCND1) modified with a guide library"
},
{
"@id": "/in-vitro-systems/IGVFSM4674ZTIR/",
"@type": [
"InVitroSystem",
"Biosample",
"Sample",
"Item"
],
"accession": "IGVFSM4674ZTIR",
"aliases": [
"jesse-engreitz:in-vitro-system_CRUDO_PILOT_CCND1-Auxin0hrs-FF1-BinF-PCR1_S78",
"jesse-engreitz:in-vitro-system_CRUDO_PILOT_CCND1-Auxin0hrs-FF1-BinF-PCR2_S174",
"jesse-engreitz:in-vitro-system_CRUDO_PILOT_CCND1-Auxin0hrs-FF1-BinF-PCR3_S270",
"jesse-engreitz:in-vitro-system_CRUDO_PILOT_CCND1-Auxin0hrs-FF1-BinF-PCR4_S366"
],
"classifications": [
"cell line"
],
"donors": [
{
"@id": "/human-donors/IGVFDO0384OZRW/",
"taxa": "Homo sapiens"
}
],
"sample_terms": [
{
"@id": "/sample-terms/EFO_0002824/",
"term_name": "HCT116"
}
],
"status": "released",
"summary": "HCT116 cell line, male, Homo sapiens (sorting details: FACS bin F for 80-100% expression of CCND1) modified with a guide library"
},
{
"@id": "/in-vitro-systems/IGVFSM4919VWFX/",
"@type": [
"InVitroSystem",
"Biosample",
"Sample",
"Item"
],
"accession": "IGVFSM4919VWFX",
"aliases": [
"jesse-engreitz:in-vitro-system_CRUDO_PILOT_CCND1-Auxin0hrs-FF1-BinD-PCR1_S76",
"jesse-engreitz:in-vitro-system_CRUDO_PILOT_CCND1-Auxin0hrs-FF1-BinD-PCR2_S172",
"jesse-engreitz:in-vitro-system_CRUDO_PILOT_CCND1-Auxin0hrs-FF1-BinD-PCR3_S268",
"jesse-engreitz:in-vitro-system_CRUDO_PILOT_CCND1-Auxin0hrs-FF1-BinD-PCR4_S364"
],
"classifications": [
"cell line"
],
"donors": [
{
"@id": "/human-donors/IGVFDO0384OZRW/",
"taxa": "Homo sapiens"
}
],
"sample_terms": [
{
"@id": "/sample-terms/EFO_0002824/",
"term_name": "HCT116"
}
],
"status": "released",
"summary": "HCT116 cell line, male, Homo sapiens (sorting details: FACS bin D for 55-65% expression of CCND1) modified with a guide library"
},
{
"@id": "/in-vitro-systems/IGVFSM0561OELB/",
"@type": [
"InVitroSystem",
"Biosample",
"Sample",
"Item"
],
"accession": "IGVFSM0561OELB",
"aliases": [
"jesse-engreitz:in-vitro-system_CRUDO_PILOT_CCND1-Auxin6hrs-FF1-BinA-PCR1_S1",
"jesse-engreitz:in-vitro-system_CRUDO_PILOT_CCND1-Auxin6hrs-FF1-BinA-PCR2_S97",
"jesse-engreitz:in-vitro-system_CRUDO_PILOT_CCND1-Auxin6hrs-FF1-BinA-PCR3_S193",
"jesse-engreitz:in-vitro-system_CRUDO_PILOT_CCND1-Auxin6hrs-FF1-BinA-PCR4_S289"
],
"classifications": [
"cell line"
],
"donors": [
{
"@id": "/human-donors/IGVFDO0384OZRW/",
"taxa": "Homo sapiens"
}
],
"sample_terms": [
{
"@id": "/sample-terms/EFO_0002824/",
"term_name": "HCT116"
}
],
"status": "released",
"summary": "HCT116 cell line, male, Homo sapiens (sorting details: FACS bin A for 0-10% expression of CCND1) treated with 1 μM 5-Phenyl-1H-indole-3-acetic acid for 6 hours, modified with a guide library"
},
{
"@id": "/in-vitro-systems/IGVFSM8104CCIE/",
"@type": [
"InVitroSystem",
"Biosample",
"Sample",
"Item"
],
"accession": "IGVFSM8104CCIE",
"aliases": [
"jesse-engreitz:in-vitro-system_CRUDO_PILOT_CCND1-Auxin6hrs-FF1-BinB-PCR1_S2",
"jesse-engreitz:in-vitro-system_CRUDO_PILOT_CCND1-Auxin6hrs-FF1-BinB-PCR2_S98",
"jesse-engreitz:in-vitro-system_CRUDO_PILOT_CCND1-Auxin6hrs-FF1-BinB-PCR3_S194",
"jesse-engreitz:in-vitro-system_CRUDO_PILOT_CCND1-Auxin6hrs-FF1-BinB-PCR4_S290"
],
"classifications": [
"cell line"
],
"donors": [
{
"@id": "/human-donors/IGVFDO0384OZRW/",
"taxa": "Homo sapiens"
}
],
"sample_terms": [
{
"@id": "/sample-terms/EFO_0002824/",
"term_name": "HCT116"
}
],
"status": "released",
"summary": "HCT116 cell line, male, Homo sapiens (sorting details: FACS bin B for 10-20% expression of CCND1) treated with 1 μM 5-Phenyl-1H-indole-3-acetic acid for 6 hours, modified with a guide library"
},
{
"@id": "/in-vitro-systems/IGVFSM7735WAOD/",
"@type": [
"InVitroSystem",
"Biosample",
"Sample",
"Item"
],
"accession": "IGVFSM7735WAOD",
"aliases": [
"jesse-engreitz:in-vitro-system_CRUDO_PILOT_CCND1-Auxin6hrs-FF1-BinD-PCR1_S4",
"jesse-engreitz:in-vitro-system_CRUDO_PILOT_CCND1-Auxin6hrs-FF1-BinD-PCR2_S100",
"jesse-engreitz:in-vitro-system_CRUDO_PILOT_CCND1-Auxin6hrs-FF1-BinD-PCR3_S196",
"jesse-engreitz:in-vitro-system_CRUDO_PILOT_CCND1-Auxin6hrs-FF1-BinD-PCR4_S292"
],
"classifications": [
"cell line"
],
"donors": [
{
"@id": "/human-donors/IGVFDO0384OZRW/",
"taxa": "Homo sapiens"
}
],
"sample_terms": [
{
"@id": "/sample-terms/EFO_0002824/",
"term_name": "HCT116"
}
],
"status": "released",
"summary": "HCT116 cell line, male, Homo sapiens (sorting details: FACS bin D for 55-65% expression of CCND1) treated with 1 μM 5-Phenyl-1H-indole-3-acetic acid for 6 hours, modified with a guide library"
},
{
"@id": "/in-vitro-systems/IGVFSM7863HHJP/",
"@type": [
"InVitroSystem",
"Biosample",
"Sample",
"Item"
],
"accession": "IGVFSM7863HHJP",
"aliases": [
"jesse-engreitz:in-vitro-system_CRUDO_PILOT_CCND1-Auxin0hrs-FF1-BinB-PCR1_S74",
"jesse-engreitz:in-vitro-system_CRUDO_PILOT_CCND1-Auxin0hrs-FF1-BinB-PCR2_S170",
"jesse-engreitz:in-vitro-system_CRUDO_PILOT_CCND1-Auxin0hrs-FF1-BinB-PCR3_S266",
"jesse-engreitz:in-vitro-system_CRUDO_PILOT_CCND1-Auxin0hrs-FF1-BinB-PCR4_S362"
],
"classifications": [
"cell line"
],
"donors": [
{
"@id": "/human-donors/IGVFDO0384OZRW/",
"taxa": "Homo sapiens"
}
],
"sample_terms": [
{
"@id": "/sample-terms/EFO_0002824/",
"term_name": "HCT116"
}
],
"status": "released",
"summary": "HCT116 cell line, male, Homo sapiens (sorting details: FACS bin B for 10-20% expression of CCND1) modified with a guide library"
}
],
"audit": {
"WARNING": [
{
"category": "missing sequencing kit",
"detail": "Construct library set [IGVFDS0392OWNZ](/construct-library-sets/IGVFDS0392OWNZ/) has sequence file(s) [IGVFFI7074ETMO](/sequence-files/IGVFFI7074ETMO/) which lack specification of a `sequencing_kit`. Sequence files should specify a sequencing kit.",
"level": 40,
"level_name": "WARNING",
"name": "audit_inconsistent_sequencing_kit",
"path": "/construct-library-sets/IGVFDS0392OWNZ/"
},
{
"category": "missing analysis",
"detail": "Construct library set [IGVFDS0392OWNZ](/construct-library-sets/IGVFDS0392OWNZ/) 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_file_set_for",
"path": "/construct-library-sets/IGVFDS0392OWNZ/"
}
]
},
"award": {
"@id": "/awards/HG011972/",
"component": "functional characterization"
},
"control_for": [],
"creation_timestamp": "2024-05-31T03:24:39.926836+00:00",
"documents": [
"/documents/4b4305ce-5844-4b84-a3c7-263a1040b050/"
],
"file_set_type": "guide library",
"files": [
{
"@id": "/sequence-files/IGVFFI7074ETMO/",
"accession": "IGVFFI7074ETMO",
"aliases": [
"jesse-engreitz:gRNAlibrary_file_CRUDO_PILOT_CCND1"
],
"content_type": "reads",
"file_format": "fastq",
"upload_status": "validated"
},
{
"@id": "/configuration-files/IGVFFI5604EFYC/",
"accession": "IGVFFI5604EFYC",
"aliases": [
"jesse-engreitz:seqspecfile_testguideseq_CRUDO_CCND1_Pilot"
],
"content_type": "seqspec",
"file_format": "yaml",
"upload_status": "validated"
}
],
"guide_type": "sgRNA",
"input_file_set_for": [],
"integrated_content_files": [
{
"@id": "/tabular-files/IGVFFI4981YFMT/",
"accession": "IGVFFI4981YFMT",
"aliases": [
"jesse-engreitz:guidedesign_file_CRUDO_PILOT_CCND1"
],
"content_type": "guide RNA sequences",
"file_format": "tsv",
"upload_status": "validated"
}
],
"lab": {
"@id": "/labs/jesse-engreitz/",
"title": "Jesse Engreitz, Stanford"
},
"release_timestamp": "2024-07-10T19:49:19.455075+00:00",
"schema_version": "9",
"scope": "loci",
"selection_criteria": [
"accessible genome regions"
],
"small_scale_loci_list": [
{
"assembly": "GRCh38",
"chromosome": "chr11",
"end": 69297814,
"start": 69296579
},
{
"assembly": "GRCh38",
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},
{
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"start": 69637976
},
{
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"chromosome": "chr11",
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"start": 69640512
},
{
"assembly": "GRCh38",
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},
{
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},
{
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},
{
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},
{
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},
{
"assembly": "GRCh38",
"chromosome": "chr2",
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"start": 181784494
},
{
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},
{
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},
{
"assembly": "GRCh38",
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},
{
"assembly": "GRCh38",
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},
{
"assembly": "GRCh38",
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},
{
"assembly": "GRCh38",
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},
{
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