{
"@context": "/terms/",
"@id": "/measurement-sets/IGVFDS3243KYES/",
"@type": [
"MeasurementSet",
"FileSet",
"Item"
],
"accession": "IGVFDS3243KYES",
"aliases": [
"jesse-engreitz:220228_8merInsertion-THP1-Amp_PPIF_promoter-BioRep3-FFrep2-BinC_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 [IGVFSM0075VGTB](/in-vitro-systems/IGVFSM0075VGTB/) 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/IGVFSM0075VGTB/"
},
{
"category": "missing publication",
"detail": "In vitro system [IGVFSM0075VGTB](/in-vitro-systems/IGVFSM0075VGTB/) 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/IGVFSM0075VGTB/"
},
{
"category": "missing publication",
"detail": "Measurement set [IGVFDS3243KYES](/measurement-sets/IGVFDS3243KYES/) 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/IGVFDS3243KYES/"
},
{
"category": "missing sequencing kit",
"detail": "Measurement set [IGVFDS3243KYES](/measurement-sets/IGVFDS3243KYES/) has sequence file(s) [IGVFFI1174PRKY](/sequence-files/IGVFFI1174PRKY/), [IGVFFI7689PKTZ](/sequence-files/IGVFFI7689PKTZ/), [IGVFFI3590GGHL](/sequence-files/IGVFFI3590GGHL/), [IGVFFI1611LAVH](/sequence-files/IGVFFI1611LAVH/), [IGVFFI7496DPOS](/sequence-files/IGVFFI7496DPOS/), [IGVFFI6057HHZR](/sequence-files/IGVFFI6057HHZR/), [IGVFFI4519IVML](/sequence-files/IGVFFI4519IVML/), [IGVFFI3182FSWX](/sequence-files/IGVFFI3182FSWX/) 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/IGVFDS3243KYES/"
},
{
"category": "missing sequence specification",
"detail": "Measurement set [IGVFDS3243KYES](/measurement-sets/IGVFDS3243KYES/) has sequence file(s): [IGVFFI1174PRKY](/sequence-files/IGVFFI1174PRKY/), [IGVFFI7689PKTZ](/sequence-files/IGVFFI7689PKTZ/), [IGVFFI3590GGHL](/sequence-files/IGVFFI3590GGHL/), [IGVFFI1611LAVH](/sequence-files/IGVFFI1611LAVH/), [IGVFFI7496DPOS](/sequence-files/IGVFFI7496DPOS/), [IGVFFI6057HHZR](/sequence-files/IGVFFI6057HHZR/), [IGVFFI4519IVML](/sequence-files/IGVFFI4519IVML/), [IGVFFI3182FSWX](/sequence-files/IGVFFI3182FSWX/) 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/IGVFDS3243KYES/"
}
],
"WARNING": [
{
"category": "missing auxiliary set",
"detail": "Measurement set [IGVFDS3243KYES](/measurement-sets/IGVFDS3243KYES/) 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/IGVFDS3243KYES/"
}
]
},
"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": "2023-11-30T22:46:32.201304+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/IGVFFI1174PRKY/",
"accession": "IGVFFI1174PRKY",
"aliases": [
"jesse-engreitz:220228_8merInsertion-THP1-Amp_PPIF_promoter-BioRep3-FFrep2-BinC-PCRrep1_R1"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2023-12-05T18:30:06.034391+00:00",
"file_format": "fastq",
"file_size": 8133692,
"href": "/sequence-files/IGVFFI1174PRKY/@@download/IGVFFI1174PRKY.fastq.gz",
"md5sum": "4d824728e0dff640aff42913e8186b95",
"s3_uri": "s3://igvf-files/2023/12/05/be493722-3f0f-450e-9920-3291177435c4/IGVFFI1174PRKY.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-FFRep2-BinC-PCRrep1_S10_R1_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI7689PKTZ/",
"accession": "IGVFFI7689PKTZ",
"aliases": [
"jesse-engreitz:220228_8merInsertion-THP1-Amp_PPIF_promoter-BioRep3-FFrep2-BinC-PCRrep2_I2"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2023-12-05T19:14:14.986021+00:00",
"file_format": "fastq",
"file_size": 2755963,
"href": "/sequence-files/IGVFFI7689PKTZ/@@download/IGVFFI7689PKTZ.fastq.gz",
"md5sum": "4826924a290135db39b1c0e7d420822f",
"s3_uri": "s3://igvf-files/2023/12/05/beb0b79c-94a5-4204-85dc-1ef0e9bf4df4/IGVFFI7689PKTZ.fastq.gz",
"sequencing_platform": {
"@id": "/platform-terms/EFO_0008566/",
"status": "released",
"term_name": "Illumina NextSeq 550"
},
"status": "released",
"submitted_file_name": "220426pPPIF_REPEAT-THP1-Gen8b-pPPIF-Amp_pPPIF-BioRep1-FFRep2-BinC-PCRrep2_S106_I2_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI3590GGHL/",
"accession": "IGVFFI3590GGHL",
"aliases": [
"jesse-engreitz:220228_8merInsertion-THP1-Amp_PPIF_promoter-BioRep3-FFrep2-BinC-PCRrep2_R1"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2023-12-05T18:36:25.012047+00:00",
"file_format": "fastq",
"file_size": 8062235,
"href": "/sequence-files/IGVFFI3590GGHL/@@download/IGVFFI3590GGHL.fastq.gz",
"md5sum": "def9ebdaa351b8ecefb19fd1638eb572",
"s3_uri": "s3://igvf-files/2023/12/05/97f82ddc-6d8f-4d64-bd7f-193e40324bdf/IGVFFI3590GGHL.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-FFRep2-BinC-PCRrep2_S106_R1_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI1611LAVH/",
"accession": "IGVFFI1611LAVH",
"aliases": [
"jesse-engreitz:220228_8merInsertion-THP1-Amp_PPIF_promoter-BioRep3-FFrep2-BinC-PCRrep2_I1"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2023-12-05T19:01:57.628737+00:00",
"file_format": "fastq",
"file_size": 2825860,
"href": "/sequence-files/IGVFFI1611LAVH/@@download/IGVFFI1611LAVH.fastq.gz",
"md5sum": "9f8093a0692cd7a3aea7f74cf518e0b6",
"s3_uri": "s3://igvf-files/2023/12/05/651e3f49-b187-4071-91f1-499fbbc2c45b/IGVFFI1611LAVH.fastq.gz",
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"status": "released",
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},
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"submitted_file_name": "220426pPPIF_REPEAT-THP1-Gen8b-pPPIF-Amp_pPPIF-BioRep1-FFRep2-BinC-PCRrep2_S106_I1_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI7496DPOS/",
"accession": "IGVFFI7496DPOS",
"aliases": [
"jesse-engreitz:220228_8merInsertion-THP1-Amp_PPIF_promoter-BioRep3-FFrep2-BinC-PCRrep1_R2"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2023-12-05T18:42:45.705355+00:00",
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"href": "/sequence-files/IGVFFI7496DPOS/@@download/IGVFFI7496DPOS.fastq.gz",
"md5sum": "aeac822ee3b0cc548fb17fb74c020e24",
"s3_uri": "s3://igvf-files/2023/12/05/3ae447c6-800c-4015-a600-7f28d7731a18/IGVFFI7496DPOS.fastq.gz",
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"status": "released",
"term_name": "Illumina NextSeq 550"
},
"status": "released",
"submitted_file_name": "220426pPPIF_REPEAT-THP1-Gen8b-pPPIF-Amp_pPPIF-BioRep1-FFRep2-BinC-PCRrep1_S10_R2_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI6057HHZR/",
"accession": "IGVFFI6057HHZR",
"aliases": [
"jesse-engreitz:220228_8merInsertion-THP1-Amp_PPIF_promoter-BioRep3-FFrep2-BinC-PCRrep1_I1"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2023-12-05T18:55:37.825482+00:00",
"file_format": "fastq",
"file_size": 2831414,
"href": "/sequence-files/IGVFFI6057HHZR/@@download/IGVFFI6057HHZR.fastq.gz",
"md5sum": "2100d61431aeb1ab490a8b13cf23027b",
"s3_uri": "s3://igvf-files/2023/12/05/15fd2e8f-2965-479d-aeea-22a5e78d3917/IGVFFI6057HHZR.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-FFRep2-BinC-PCRrep1_S10_I1_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI4519IVML/",
"accession": "IGVFFI4519IVML",
"aliases": [
"jesse-engreitz:220228_8merInsertion-THP1-Amp_PPIF_promoter-BioRep3-FFrep2-BinC-PCRrep2_R2"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2023-12-05T18:49:10.129182+00:00",
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"md5sum": "e0a40d0981f48d2972aec52105514e78",
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"status": "released",
"term_name": "Illumina NextSeq 550"
},
"status": "released",
"submitted_file_name": "220426pPPIF_REPEAT-THP1-Gen8b-pPPIF-Amp_pPPIF-BioRep1-FFRep2-BinC-PCRrep2_S106_R2_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI3182FSWX/",
"accession": "IGVFFI3182FSWX",
"aliases": [
"jesse-engreitz:220228_8merInsertion-THP1-Amp_PPIF_promoter-BioRep3-FFrep2-BinC-PCRrep1_I2"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2023-12-05T19:08:04.910896+00:00",
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"md5sum": "e33196460e642226a562699ea4f2fa5c",
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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-FFRep2-BinC-PCRrep1_S10_I2_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": "2023-12-20T23:09:43.237253+00:00",
"samples": [
{
"@id": "/in-vitro-systems/IGVFSM0075VGTB/",
"@type": [
"InVitroSystem",
"Biosample",
"Sample",
"Item"
],
"accession": "IGVFSM0075VGTB",
"aliases": [
"jesse-engreitz:220228_8merInsertion-THP1-Amp_PPIF_promoter-BioRep3-FFrep2-BinC"
],
"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 35-45% 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": "2023-12-05T18:30:06.034391+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": "2ca5ff61-4dc1-48d4-8b71-e25f3789edbc"
}