{
"@context": "/terms/",
"@id": "/measurement-sets/IGVFDS7530NWPC/",
"@type": [
"MeasurementSet",
"FileSet",
"Item"
],
"accession": "IGVFDS7530NWPC",
"aliases": [
"jesse-engreitz:220228_8merInsertion-THP1-Amp_PPIF_promoter-BioRep4-FFrep1-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 [IGVFSM0484FSRU](/in-vitro-systems/IGVFSM0484FSRU/) 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/IGVFSM0484FSRU/"
},
{
"category": "missing publication",
"detail": "In vitro system [IGVFSM0484FSRU](/in-vitro-systems/IGVFSM0484FSRU/) 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/IGVFSM0484FSRU/"
},
{
"category": "missing publication",
"detail": "Measurement set [IGVFDS7530NWPC](/measurement-sets/IGVFDS7530NWPC/) 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/IGVFDS7530NWPC/"
},
{
"category": "missing sequencing kit",
"detail": "Measurement set [IGVFDS7530NWPC](/measurement-sets/IGVFDS7530NWPC/) has sequence file(s) [IGVFFI3473JJPZ](/sequence-files/IGVFFI3473JJPZ/), [IGVFFI4378ANRF](/sequence-files/IGVFFI4378ANRF/), [IGVFFI1262OQKB](/sequence-files/IGVFFI1262OQKB/), [IGVFFI2642IERI](/sequence-files/IGVFFI2642IERI/), [IGVFFI2046ODIY](/sequence-files/IGVFFI2046ODIY/), [IGVFFI4060HNVI](/sequence-files/IGVFFI4060HNVI/), [IGVFFI6874GKUW](/sequence-files/IGVFFI6874GKUW/), [IGVFFI3509FEJS](/sequence-files/IGVFFI3509FEJS/) 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/IGVFDS7530NWPC/"
},
{
"category": "missing sequence specification",
"detail": "Measurement set [IGVFDS7530NWPC](/measurement-sets/IGVFDS7530NWPC/) has sequence file(s): [IGVFFI3473JJPZ](/sequence-files/IGVFFI3473JJPZ/), [IGVFFI4378ANRF](/sequence-files/IGVFFI4378ANRF/), [IGVFFI1262OQKB](/sequence-files/IGVFFI1262OQKB/), [IGVFFI2642IERI](/sequence-files/IGVFFI2642IERI/), [IGVFFI2046ODIY](/sequence-files/IGVFFI2046ODIY/), [IGVFFI4060HNVI](/sequence-files/IGVFFI4060HNVI/), [IGVFFI6874GKUW](/sequence-files/IGVFFI6874GKUW/), [IGVFFI3509FEJS](/sequence-files/IGVFFI3509FEJS/) 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/IGVFDS7530NWPC/"
}
],
"WARNING": [
{
"category": "missing auxiliary set",
"detail": "Measurement set [IGVFDS7530NWPC](/measurement-sets/IGVFDS7530NWPC/) 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/IGVFDS7530NWPC/"
}
]
},
"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": "2023-11-30T22:46:44.403079+00:00",
"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/IGVFFI3473JJPZ/",
"accession": "IGVFFI3473JJPZ",
"aliases": [
"jesse-engreitz:220228_8merInsertion-THP1-Amp_PPIF_promoter-BioRep4-FFrep1-BinC-PCRrep2_R2"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2023-12-05T18:51:21.921082+00:00",
"file_format": "fastq",
"file_size": 17434126,
"href": "/sequence-files/IGVFFI3473JJPZ/@@download/IGVFFI3473JJPZ.fastq.gz",
"s3_uri": "s3://igvf-files/2023/12/05/a728d95f-22cc-43d6-b695-61eb7d21b315/IGVFFI3473JJPZ.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-BioRep2-FFRep1-BinC-PCRrep2_S120_R2_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI4378ANRF/",
"accession": "IGVFFI4378ANRF",
"aliases": [
"jesse-engreitz:220228_8merInsertion-THP1-Amp_PPIF_promoter-BioRep4-FFrep1-BinC-PCRrep1_I2"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2023-12-05T19:10:06.874514+00:00",
"file_format": "fastq",
"file_size": 2719295,
"href": "/sequence-files/IGVFFI4378ANRF/@@download/IGVFFI4378ANRF.fastq.gz",
"s3_uri": "s3://igvf-files/2023/12/05/49a2fce8-6da8-44f6-b60b-2c1e998d326a/IGVFFI4378ANRF.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-BioRep2-FFRep1-BinC-PCRrep1_S24_I2_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI1262OQKB/",
"accession": "IGVFFI1262OQKB",
"aliases": [
"jesse-engreitz:220228_8merInsertion-THP1-Amp_PPIF_promoter-BioRep4-FFrep1-BinC-PCRrep1_I1"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2023-12-05T18:57:41.279510+00:00",
"file_format": "fastq",
"file_size": 2779857,
"href": "/sequence-files/IGVFFI1262OQKB/@@download/IGVFFI1262OQKB.fastq.gz",
"s3_uri": "s3://igvf-files/2023/12/05/2224ab07-1604-4555-bf56-43b65546864b/IGVFFI1262OQKB.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-BioRep2-FFRep1-BinC-PCRrep1_S24_I1_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI2642IERI/",
"accession": "IGVFFI2642IERI",
"aliases": [
"jesse-engreitz:220228_8merInsertion-THP1-Amp_PPIF_promoter-BioRep4-FFrep1-BinC-PCRrep2_I1"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2023-12-05T19:04:02.270057+00:00",
"file_format": "fastq",
"file_size": 2960853,
"href": "/sequence-files/IGVFFI2642IERI/@@download/IGVFFI2642IERI.fastq.gz",
"s3_uri": "s3://igvf-files/2023/12/05/0a2ca118-5570-46b5-be23-c543520dacbe/IGVFFI2642IERI.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-BioRep2-FFRep1-BinC-PCRrep2_S120_I1_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI2046ODIY/",
"accession": "IGVFFI2046ODIY",
"aliases": [
"jesse-engreitz:220228_8merInsertion-THP1-Amp_PPIF_promoter-BioRep4-FFrep1-BinC-PCRrep2_R1"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2023-12-05T18:38:30.861378+00:00",
"file_format": "fastq",
"file_size": 8616264,
"href": "/sequence-files/IGVFFI2046ODIY/@@download/IGVFFI2046ODIY.fastq.gz",
"s3_uri": "s3://igvf-files/2023/12/05/e7b90d7c-d059-4bbf-ab77-9b0d6945c989/IGVFFI2046ODIY.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-BioRep2-FFRep1-BinC-PCRrep2_S120_R1_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI4060HNVI/",
"accession": "IGVFFI4060HNVI",
"aliases": [
"jesse-engreitz:220228_8merInsertion-THP1-Amp_PPIF_promoter-BioRep4-FFrep1-BinC-PCRrep2_I2"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2023-12-05T19:16:17.824662+00:00",
"file_format": "fastq",
"file_size": 2917383,
"href": "/sequence-files/IGVFFI4060HNVI/@@download/IGVFFI4060HNVI.fastq.gz",
"s3_uri": "s3://igvf-files/2023/12/05/91545981-3cba-4e27-a59e-219054f97f83/IGVFFI4060HNVI.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-BioRep2-FFRep1-BinC-PCRrep2_S120_I2_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI6874GKUW/",
"accession": "IGVFFI6874GKUW",
"aliases": [
"jesse-engreitz:220228_8merInsertion-THP1-Amp_PPIF_promoter-BioRep4-FFrep1-BinC-PCRrep1_R2"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2023-12-05T18:44:54.028717+00:00",
"file_format": "fastq",
"file_size": 15937031,
"href": "/sequence-files/IGVFFI6874GKUW/@@download/IGVFFI6874GKUW.fastq.gz",
"s3_uri": "s3://igvf-files/2023/12/05/6ef9d330-9939-4db3-a90f-23925a502b3b/IGVFFI6874GKUW.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-BioRep2-FFRep1-BinC-PCRrep1_S24_R2_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI3509FEJS/",
"accession": "IGVFFI3509FEJS",
"aliases": [
"jesse-engreitz:220228_8merInsertion-THP1-Amp_PPIF_promoter-BioRep4-FFrep1-BinC-PCRrep1_R1"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2023-12-05T18:32:14.554643+00:00",
"file_format": "fastq",
"file_size": 8174615,
"href": "/sequence-files/IGVFFI3509FEJS/@@download/IGVFFI3509FEJS.fastq.gz",
"s3_uri": "s3://igvf-files/2023/12/05/b3f03ba6-3087-4a1b-a8d0-8787de91b2ae/IGVFFI3509FEJS.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-BioRep2-FFRep1-BinC-PCRrep1_S24_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": "2023-12-20T23:10:04.474992+00:00",
"samples": [
{
"@id": "/in-vitro-systems/IGVFSM0484FSRU/",
"@type": [
"InVitroSystem",
"Biosample",
"Sample",
"Item"
],
"accession": "IGVFSM0484FSRU",
"aliases": [
"jesse-engreitz:220228_8merInsertion-THP1-Amp_PPIF_promoter-BioRep4-FFrep1-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": "2023-12-05T18:32:14.554643+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": "8691bb52-38e9-4b7e-b8d1-89e44d6d8aec"
}