{
"@context": "/terms/",
"@id": "/measurement-sets/IGVFDS6214RDRM/",
"@type": [
"MeasurementSet",
"FileSet",
"Item"
],
"accession": "IGVFDS6214RDRM",
"aliases": [
"jesse-engreitz:220228_8merInsertion-THP1-Amp_PPIF_promoter-BioRep3-FFrep1-BinE_AmpliconSequencing"
],
"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": "mismatched status",
"detail": "Released in vitro system [IGVFSM6445TGKO](/in-vitro-systems/IGVFSM6445TGKO/) has in progress subobject construct library set [IGVFDS6377KNCH](/construct-library-sets/IGVFDS6377KNCH/).",
"level": 30,
"level_name": "INTERNAL_ACTION",
"name": "audit_item_status",
"path": "/in-vitro-systems/IGVFSM6445TGKO/"
},
{
"category": "missing publication",
"detail": "In vitro system [IGVFSM6445TGKO](/in-vitro-systems/IGVFSM6445TGKO/) 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/IGVFSM6445TGKO/"
},
{
"category": "missing publication",
"detail": "Measurement set [IGVFDS6214RDRM](/measurement-sets/IGVFDS6214RDRM/) 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/IGVFDS6214RDRM/"
},
{
"category": "missing sequencing kit",
"detail": "Measurement set [IGVFDS6214RDRM](/measurement-sets/IGVFDS6214RDRM/) has sequence file(s) [IGVFFI8734GGIO](/sequence-files/IGVFFI8734GGIO/), [IGVFFI5637DQIA](/sequence-files/IGVFFI5637DQIA/), [IGVFFI9203XPXF](/sequence-files/IGVFFI9203XPXF/), [IGVFFI3039ZYBX](/sequence-files/IGVFFI3039ZYBX/), [IGVFFI1890UWCK](/sequence-files/IGVFFI1890UWCK/), [IGVFFI1019ALHZ](/sequence-files/IGVFFI1019ALHZ/), [IGVFFI5390TVFX](/sequence-files/IGVFFI5390TVFX/), [IGVFFI4335SIPP](/sequence-files/IGVFFI4335SIPP/) 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/IGVFDS6214RDRM/"
},
{
"category": "missing sequence specification",
"detail": "Measurement set [IGVFDS6214RDRM](/measurement-sets/IGVFDS6214RDRM/) has sequence file(s): [IGVFFI8734GGIO](/sequence-files/IGVFFI8734GGIO/), [IGVFFI5637DQIA](/sequence-files/IGVFFI5637DQIA/), [IGVFFI9203XPXF](/sequence-files/IGVFFI9203XPXF/), [IGVFFI3039ZYBX](/sequence-files/IGVFFI3039ZYBX/), [IGVFFI1890UWCK](/sequence-files/IGVFFI1890UWCK/), [IGVFFI1019ALHZ](/sequence-files/IGVFFI1019ALHZ/), [IGVFFI5390TVFX](/sequence-files/IGVFFI5390TVFX/), [IGVFFI4335SIPP](/sequence-files/IGVFFI4335SIPP/) which do not have any `seqspecs`. Sequence files in a file set associated with bulk data are expected to link to a sequence specification file.",
"level": 30,
"level_name": "INTERNAL_ACTION",
"name": "audit_missing_seqspec",
"path": "/measurement-sets/IGVFDS6214RDRM/"
}
],
"WARNING": [
{
"category": "missing auxiliary set",
"detail": "Measurement set [IGVFDS6214RDRM](/measurement-sets/IGVFDS6214RDRM/) has no cell sorting `auxiliary_sets`. CRISPR-based measurement sets that utilize flow cytometry are expected to link to a cell sorting auxiliary set.",
"level": 40,
"level_name": "WARNING",
"name": "audit_missing_auxiliary_set",
"path": "/measurement-sets/IGVFDS6214RDRM/"
}
]
},
"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/IGVFDS6377KNCH/",
"accession": "IGVFDS6377KNCH",
"file_set_type": "guide library",
"status": "in progress",
"summary": "guide (sgRNA) library targeting sequence variants in a genomic locus"
}
],
"control_file_sets": [
{
"@id": "/measurement-sets/IGVFDS6385JXFZ/",
"accession": "IGVFDS6385JXFZ",
"aliases": [
"jesse-engreitz:220228_8merInsertion-THP1-Amp_PPIF_promoter-THP1-PE2_Exp3_NegControl_AmpliconSequencing"
],
"status": "released"
}
],
"control_for": [],
"creation_timestamp": "2023-11-30T22:46:27.740659+00:00",
"data_use_limitation_summaries": [
"no certificate"
],
"donors": [
{
"@id": "/human-donors/IGVFDO7359LVPI/",
"accession": "IGVFDO7359LVPI",
"aliases": [
"igvf:donor_of_THP1"
],
"sex": "male",
"status": "released",
"taxa": "Homo sapiens"
}
],
"externally_hosted": false,
"file_set_type": "experimental data",
"files": [
{
"@id": "/sequence-files/IGVFFI8734GGIO/",
"accession": "IGVFFI8734GGIO",
"aliases": [
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],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2023-12-05T19:01:14.056809+00:00",
"file_format": "fastq",
"file_size": 2923729,
"href": "/sequence-files/IGVFFI8734GGIO/@@download/IGVFFI8734GGIO.fastq.gz",
"md5sum": "27ee7132ba8ddad3557ecb55003bd635",
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"sequencing_platform": {
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"status": "released",
"term_name": "Illumina NextSeq 550"
},
"status": "released",
"submitted_file_name": "220426pPPIF_REPEAT-THP1-Gen8b-pPPIF-Amp_pPPIF-BioRep1-FFRep1-BinE-PCRrep2_S101_I1_001.fastq.gz",
"upload_status": "validated"
},
{
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"accession": "IGVFFI5637DQIA",
"aliases": [
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],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2023-12-05T18:29:20.845465+00:00",
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"md5sum": "0850dc1ceaf98c19f5b5e5d9303c72db",
"s3_uri": "s3://igvf-files/2023/12/05/e0802501-b719-4467-89cc-e39bd5820ba0/IGVFFI5637DQIA.fastq.gz",
"sequencing_platform": {
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"status": "released",
"term_name": "Illumina NextSeq 550"
},
"status": "released",
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"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI9203XPXF/",
"accession": "IGVFFI9203XPXF",
"aliases": [
"jesse-engreitz:220228_8merInsertion-THP1-Amp_PPIF_promoter-BioRep3-FFrep1-BinE-PCRrep2_I2"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2023-12-05T19:13:31.411352+00:00",
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"href": "/sequence-files/IGVFFI9203XPXF/@@download/IGVFFI9203XPXF.fastq.gz",
"md5sum": "2acf167291dc646433b31a7d44057636",
"s3_uri": "s3://igvf-files/2023/12/05/06e09b0b-f00a-4e98-83c6-a96ff583948d/IGVFFI9203XPXF.fastq.gz",
"sequencing_platform": {
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"status": "released",
"term_name": "Illumina NextSeq 550"
},
"status": "released",
"submitted_file_name": "220426pPPIF_REPEAT-THP1-Gen8b-pPPIF-Amp_pPPIF-BioRep1-FFRep1-BinE-PCRrep2_S101_I2_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI3039ZYBX/",
"accession": "IGVFFI3039ZYBX",
"aliases": [
"jesse-engreitz:220228_8merInsertion-THP1-Amp_PPIF_promoter-BioRep3-FFrep1-BinE-PCRrep1_I1"
],
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"creation_timestamp": "2023-12-05T18:54:54.204565+00:00",
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"href": "/sequence-files/IGVFFI3039ZYBX/@@download/IGVFFI3039ZYBX.fastq.gz",
"md5sum": "e1eb1425b0cc40331d57a50a0780f193",
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"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI1890UWCK/",
"accession": "IGVFFI1890UWCK",
"aliases": [
"jesse-engreitz:220228_8merInsertion-THP1-Amp_PPIF_promoter-BioRep3-FFrep1-BinE-PCRrep1_I2"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2023-12-05T19:07:21.588707+00:00",
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"md5sum": "8a3caac6be94fee195c2068b0dc529ee",
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"status": "released",
"term_name": "Illumina NextSeq 550"
},
"status": "released",
"submitted_file_name": "220426pPPIF_REPEAT-THP1-Gen8b-pPPIF-Amp_pPPIF-BioRep1-FFRep1-BinE-PCRrep1_S5_I2_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI1019ALHZ/",
"accession": "IGVFFI1019ALHZ",
"aliases": [
"jesse-engreitz:220228_8merInsertion-THP1-Amp_PPIF_promoter-BioRep3-FFrep1-BinE-PCRrep2_R2"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2023-12-05T18:48:24.242128+00:00",
"file_format": "fastq",
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"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI5390TVFX/",
"accession": "IGVFFI5390TVFX",
"aliases": [
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],
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"term_name": "Illumina NextSeq 550"
},
"status": "released",
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"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI4335SIPP/",
"accession": "IGVFFI4335SIPP",
"aliases": [
"jesse-engreitz:220228_8merInsertion-THP1-Amp_PPIF_promoter-BioRep3-FFrep1-BinE-PCRrep2_R1"
],
"content_type": "reads",
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"creation_timestamp": "2023-12-05T18:35:40.547270+00:00",
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"status": "released",
"term_name": "Illumina NextSeq 550"
},
"status": "released",
"submitted_file_name": "220426pPPIF_REPEAT-THP1-Gen8b-pPPIF-Amp_pPPIF-BioRep1-FFRep1-BinE-PCRrep2_S101_R1_001.fastq.gz",
"upload_status": "validated"
}
],
"input_for": [
"/analysis-sets/IGVFDS5056OAGR/"
],
"lab": {
"@id": "/labs/jesse-engreitz/",
"title": "Jesse Engreitz, Stanford"
},
"notes": "The readout 2e41e624-f6c7-4f0c-a07e-bc36cefdca39 was removed from this measurement set. This measurement set previously used Variant FlowFISH as a preferred_assay_title, but this enum is now removed. So it has been defaulted to Variant-EFFECTS.",
"preferred_assay_title": "Variant-EFFECTS",
"protocols": [
"https://www.protocols.io/view/flowfish-with-primeflow-36wgq3q4olk5/v1"
],
"release_timestamp": "2023-12-20T23:09:16.633601+00:00",
"samples": [
{
"@id": "/in-vitro-systems/IGVFSM6445TGKO/",
"@type": [
"InVitroSystem",
"Biosample",
"Sample",
"Item"
],
"accession": "IGVFSM6445TGKO",
"aliases": [
"jesse-engreitz:220228_8merInsertion-THP1-Amp_PPIF_promoter-BioRep3-FFrep1-BinE"
],
"classifications": [
"cell line"
],
"institutional_certificates": [],
"modifications": [
{
"@id": "/crispr-modifications/fc6bc0b3-a064-47d0-b95d-a9af14bb1624/",
"modality": "prime editing",
"status": "released"
}
],
"sample_terms": [
{
"@id": "/sample-terms/EFO_0001253/",
"@type": [
"SampleTerm",
"OntologyTerm",
"Item"
],
"aliases": [
"igvf:THP-1"
],
"status": "released",
"summary": "THP-1",
"term_name": "THP-1"
}
],
"status": "released",
"summary": "Homo sapiens (male) THP-1 cell line (sorting details: FACS bin for 80-90% expression of PPIF) modified with CRISPR prime editing Sp-nCas9-M-MLV RT (PE2), transduced (lentivirus) with a guide library",
"taxa": "Homo sapiens"
}
],
"schema_version": "26",
"status": "released",
"submitted_by": {
"@id": "/users/f9e7cd82-a407-4a20-89ee-f4dc668b0cbe/",
"title": "Michael Montgomery"
},
"submitted_files_timestamp": "2023-12-05T18:29:20.845465+00:00",
"summary": "CRISPR prime editing Variant-EFFECTS sorted on the expression of PPIF integrating a guide (sgRNA) library targeting sequence variants in a genomic locus",
"targeted_genes": [
{
"@id": "/genes/ENSG00000108179/",
"geneid": "ENSG00000108179",
"name": "peptidylprolyl isomerase F",
"status": "released",
"symbol": "PPIF",
"synonyms": [
"PPIase F",
"peptidylprolyl isomerase F",
"Cyp-D",
"peptidyl-prolyl cis-trans isomerase F, mitochondrial",
"PPIF",
"CyP-M",
"cyclophilin F",
"peptidyl-prolyl cis-trans isomerase, mitochondrial",
"cyclophilin 3",
"cyclophilin D",
"rotamase F",
"mitochondrial cyclophilin",
"CypD",
"CYP3"
]
}
],
"uuid": "69bf1ef5-c554-4c84-91c9-09447e97a9c6"
}