{
"@context": "/terms/",
"@id": "/measurement-sets/IGVFDS8801DBGC/",
"@type": [
"MeasurementSet",
"FileSet",
"Item"
],
"accession": "IGVFDS8801DBGC",
"aliases": [
"jesse-engreitz:230807S022-THP1-P153-Amp_PPIF_promoter-BioRep1-FFrep2-BinB_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 [IGVFSM9821NUGZ](/in-vitro-systems/IGVFSM9821NUGZ/) has in progress subobject construct library set [IGVFDS6982DESN](/construct-library-sets/IGVFDS6982DESN/).",
"level": 30,
"level_name": "INTERNAL_ACTION",
"name": "audit_item_status",
"path": "/in-vitro-systems/IGVFSM9821NUGZ/"
},
{
"category": "missing publication",
"detail": "In vitro system [IGVFSM9821NUGZ](/in-vitro-systems/IGVFSM9821NUGZ/) 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/IGVFSM9821NUGZ/"
},
{
"category": "missing publication",
"detail": "Measurement set [IGVFDS8801DBGC](/measurement-sets/IGVFDS8801DBGC/) 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/IGVFDS8801DBGC/"
},
{
"category": "missing sequencing kit",
"detail": "Measurement set [IGVFDS8801DBGC](/measurement-sets/IGVFDS8801DBGC/) has sequence file(s) [IGVFFI2511HHWV](/sequence-files/IGVFFI2511HHWV/), [IGVFFI4799POLJ](/sequence-files/IGVFFI4799POLJ/), [IGVFFI6987PYVU](/sequence-files/IGVFFI6987PYVU/), [IGVFFI2230HXJX](/sequence-files/IGVFFI2230HXJX/), [IGVFFI1219MIZS](/sequence-files/IGVFFI1219MIZS/), [IGVFFI0487MDHQ](/sequence-files/IGVFFI0487MDHQ/), [IGVFFI8567AQIB](/sequence-files/IGVFFI8567AQIB/), [IGVFFI1100RGNN](/sequence-files/IGVFFI1100RGNN/), [IGVFFI5689DZIF](/sequence-files/IGVFFI5689DZIF/), [IGVFFI1980UKSO](/sequence-files/IGVFFI1980UKSO/), [IGVFFI6703OOQS](/sequence-files/IGVFFI6703OOQS/), [IGVFFI8647WRKN](/sequence-files/IGVFFI8647WRKN/), [IGVFFI0026XYHX](/sequence-files/IGVFFI0026XYHX/), [IGVFFI8412BFVI](/sequence-files/IGVFFI8412BFVI/), [IGVFFI7509DXJJ](/sequence-files/IGVFFI7509DXJJ/), [IGVFFI8198VMBL](/sequence-files/IGVFFI8198VMBL/), [IGVFFI1010FOHO](/sequence-files/IGVFFI1010FOHO/), [IGVFFI5386HBNE](/sequence-files/IGVFFI5386HBNE/), [IGVFFI6861KUPN](/sequence-files/IGVFFI6861KUPN/), [IGVFFI9868IZYB](/sequence-files/IGVFFI9868IZYB/), [IGVFFI7761QWXX](/sequence-files/IGVFFI7761QWXX/), [IGVFFI0432XJBC](/sequence-files/IGVFFI0432XJBC/), [IGVFFI2644ZHUF](/sequence-files/IGVFFI2644ZHUF/), [IGVFFI4396KQKD](/sequence-files/IGVFFI4396KQKD/), [IGVFFI6197UYYS](/sequence-files/IGVFFI6197UYYS/), [IGVFFI7140KHBT](/sequence-files/IGVFFI7140KHBT/), [IGVFFI6727MQUJ](/sequence-files/IGVFFI6727MQUJ/), [IGVFFI6776PHVX](/sequence-files/IGVFFI6776PHVX/), [IGVFFI8559QBWD](/sequence-files/IGVFFI8559QBWD/), [IGVFFI3085SRIY](/sequence-files/IGVFFI3085SRIY/), [IGVFFI3136BPWN](/sequence-files/IGVFFI3136BPWN/), [IGVFFI0311LGJK](/sequence-files/IGVFFI0311LGJK/), [IGVFFI4903IIIV](/sequence-files/IGVFFI4903IIIV/), [IGVFFI2657QCJU](/sequence-files/IGVFFI2657QCJU/), [IGVFFI9623RKZT](/sequence-files/IGVFFI9623RKZT/), [IGVFFI7436QGDG](/sequence-files/IGVFFI7436QGDG/), [IGVFFI4465GIST](/sequence-files/IGVFFI4465GIST/), [IGVFFI6779DBYF](/sequence-files/IGVFFI6779DBYF/), [IGVFFI1611ZEBC](/sequence-files/IGVFFI1611ZEBC/), [IGVFFI6702WGSO](/sequence-files/IGVFFI6702WGSO/), [IGVFFI4596NTOL](/sequence-files/IGVFFI4596NTOL/), [IGVFFI4533SCBF](/sequence-files/IGVFFI4533SCBF/), [IGVFFI6164VMWT](/sequence-files/IGVFFI6164VMWT/), [IGVFFI3027QCYB](/sequence-files/IGVFFI3027QCYB/), [IGVFFI9206NPUT](/sequence-files/IGVFFI9206NPUT/), [IGVFFI4745CWBD](/sequence-files/IGVFFI4745CWBD/), [IGVFFI1713PMGU](/sequence-files/IGVFFI1713PMGU/), [IGVFFI1757NMDP](/sequence-files/IGVFFI1757NMDP/) 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/IGVFDS8801DBGC/"
},
{
"category": "missing sequence specification",
"detail": "Measurement set [IGVFDS8801DBGC](/measurement-sets/IGVFDS8801DBGC/) has sequence file(s): [IGVFFI2511HHWV](/sequence-files/IGVFFI2511HHWV/), [IGVFFI4799POLJ](/sequence-files/IGVFFI4799POLJ/), [IGVFFI6987PYVU](/sequence-files/IGVFFI6987PYVU/), [IGVFFI2230HXJX](/sequence-files/IGVFFI2230HXJX/), [IGVFFI1219MIZS](/sequence-files/IGVFFI1219MIZS/), [IGVFFI0487MDHQ](/sequence-files/IGVFFI0487MDHQ/), [IGVFFI8567AQIB](/sequence-files/IGVFFI8567AQIB/), [IGVFFI1100RGNN](/sequence-files/IGVFFI1100RGNN/), [IGVFFI5689DZIF](/sequence-files/IGVFFI5689DZIF/), [IGVFFI1980UKSO](/sequence-files/IGVFFI1980UKSO/), [IGVFFI6703OOQS](/sequence-files/IGVFFI6703OOQS/), [IGVFFI8647WRKN](/sequence-files/IGVFFI8647WRKN/), [IGVFFI0026XYHX](/sequence-files/IGVFFI0026XYHX/), [IGVFFI8412BFVI](/sequence-files/IGVFFI8412BFVI/), [IGVFFI7509DXJJ](/sequence-files/IGVFFI7509DXJJ/), [IGVFFI8198VMBL](/sequence-files/IGVFFI8198VMBL/), [IGVFFI1010FOHO](/sequence-files/IGVFFI1010FOHO/), [IGVFFI5386HBNE](/sequence-files/IGVFFI5386HBNE/), [IGVFFI6861KUPN](/sequence-files/IGVFFI6861KUPN/), [IGVFFI9868IZYB](/sequence-files/IGVFFI9868IZYB/), [IGVFFI7761QWXX](/sequence-files/IGVFFI7761QWXX/), [IGVFFI0432XJBC](/sequence-files/IGVFFI0432XJBC/), [IGVFFI2644ZHUF](/sequence-files/IGVFFI2644ZHUF/), [IGVFFI4396KQKD](/sequence-files/IGVFFI4396KQKD/), [IGVFFI6197UYYS](/sequence-files/IGVFFI6197UYYS/), [IGVFFI7140KHBT](/sequence-files/IGVFFI7140KHBT/), [IGVFFI6727MQUJ](/sequence-files/IGVFFI6727MQUJ/), [IGVFFI6776PHVX](/sequence-files/IGVFFI6776PHVX/), [IGVFFI8559QBWD](/sequence-files/IGVFFI8559QBWD/), [IGVFFI3085SRIY](/sequence-files/IGVFFI3085SRIY/), [IGVFFI3136BPWN](/sequence-files/IGVFFI3136BPWN/), [IGVFFI0311LGJK](/sequence-files/IGVFFI0311LGJK/), [IGVFFI4903IIIV](/sequence-files/IGVFFI4903IIIV/), [IGVFFI2657QCJU](/sequence-files/IGVFFI2657QCJU/), [IGVFFI9623RKZT](/sequence-files/IGVFFI9623RKZT/), [IGVFFI7436QGDG](/sequence-files/IGVFFI7436QGDG/), [IGVFFI4465GIST](/sequence-files/IGVFFI4465GIST/), [IGVFFI6779DBYF](/sequence-files/IGVFFI6779DBYF/), [IGVFFI1611ZEBC](/sequence-files/IGVFFI1611ZEBC/), [IGVFFI6702WGSO](/sequence-files/IGVFFI6702WGSO/), [IGVFFI4596NTOL](/sequence-files/IGVFFI4596NTOL/), [IGVFFI4533SCBF](/sequence-files/IGVFFI4533SCBF/), [IGVFFI6164VMWT](/sequence-files/IGVFFI6164VMWT/), [IGVFFI3027QCYB](/sequence-files/IGVFFI3027QCYB/), [IGVFFI9206NPUT](/sequence-files/IGVFFI9206NPUT/), [IGVFFI4745CWBD](/sequence-files/IGVFFI4745CWBD/), [IGVFFI1713PMGU](/sequence-files/IGVFFI1713PMGU/), [IGVFFI1757NMDP](/sequence-files/IGVFFI1757NMDP/) 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/IGVFDS8801DBGC/"
}
],
"WARNING": [
{
"category": "missing auxiliary set",
"detail": "Measurement set [IGVFDS8801DBGC](/measurement-sets/IGVFDS8801DBGC/) 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/IGVFDS8801DBGC/"
}
]
},
"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/IGVFDS6982DESN/",
"accession": "IGVFDS6982DESN",
"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/IGVFDS5864UGFT/",
"accession": "IGVFDS5864UGFT",
"aliases": [
"jesse-engreitz:230807S022-THP1-P153-Amp_PPIF_promoter-THP1-PE2_Exp2_NegControl_AmpliconSequencing"
],
"status": "released"
}
],
"control_for": [],
"creation_timestamp": "2023-11-30T22:49:37.837931+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": [
{
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"accession": "IGVFFI2511HHWV",
"aliases": [
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],
"content_type": "reads",
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"sequencing_platform": {
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"term_name": "Illumina NextSeq 550"
},
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"upload_status": "validated"
},
{
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"accession": "IGVFFI4799POLJ",
"aliases": [
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],
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},
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"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI6987PYVU/",
"accession": "IGVFFI6987PYVU",
"aliases": [
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],
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},
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},
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},
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},
{
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"aliases": [
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},
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},
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},
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"upload_status": "validated"
},
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],
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"upload_status": "validated"
},
{
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],
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"jesse-engreitz:230807S022-THP1-P153-Amp_PPIF_promoter-BioRep1-FFrep2-BinB-PCRrep2_I1"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2023-12-05T20:10:25.974292+00:00",
"file_format": "fastq",
"file_size": 2460511,
"href": "/sequence-files/IGVFFI1757NMDP/@@download/IGVFFI1757NMDP.fastq.gz",
"md5sum": "65b0ab80fbbb64fe5fe3be0e82f996cc",
"s3_uri": "s3://igvf-files/2023/12/05/e0b087da-d8ed-40b5-9991-3995fa631119/IGVFFI1757NMDP.fastq.gz",
"sequencing_platform": {
"@id": "/platform-terms/EFO_0008566/",
"status": "released",
"term_name": "Illumina NextSeq 550"
},
"status": "released",
"submitted_file_name": "230807S022-THP1-P153-Amp_PPIF_promoter-BioRep1-FFrep2-BinB-PCRrep2_S62_I1_001.fastq.gz",
"upload_status": "validated"
}
],
"input_for": [
"/analysis-sets/IGVFDS3423PSID/"
],
"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": "2023-12-20T23:06:08.502892+00:00",
"samples": [
{
"@id": "/in-vitro-systems/IGVFSM9821NUGZ/",
"@type": [
"InVitroSystem",
"Biosample",
"Sample",
"Item"
],
"accession": "IGVFSM9821NUGZ",
"aliases": [
"jesse-engreitz:230807S022-THP1-P153-Amp_PPIF_promoter-BioRep1-FFrep2-BinB"
],
"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 26-50% 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": "2023-12-05T20:08:02.068500+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": "981ac8f9-800b-4859-bf5c-e65dc3a68176"
}