{
"@context": "/terms/",
"@id": "/measurement-sets/IGVFDS6085VVNC/",
"@type": [
"MeasurementSet",
"FileSet",
"Item"
],
"accession": "IGVFDS6085VVNC",
"aliases": [
"jesse-engreitz:220829_8merInsertion-Jurkat_Stimulation-Amp_PPIF_promoter-BioRep1-FFrep2-BinA_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": "missing publication",
"detail": "Measurement set [IGVFDS6085VVNC](/measurement-sets/IGVFDS6085VVNC/) 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/IGVFDS6085VVNC/"
},
{
"category": "missing sequencing kit",
"detail": "Measurement set [IGVFDS6085VVNC](/measurement-sets/IGVFDS6085VVNC/) has sequence file(s) [IGVFFI9152EMSR](/sequence-files/IGVFFI9152EMSR/), [IGVFFI9927UHCN](/sequence-files/IGVFFI9927UHCN/), [IGVFFI0594ANPV](/sequence-files/IGVFFI0594ANPV/), [IGVFFI2437ZQEH](/sequence-files/IGVFFI2437ZQEH/), [IGVFFI5430ZDLE](/sequence-files/IGVFFI5430ZDLE/), [IGVFFI6834BFYY](/sequence-files/IGVFFI6834BFYY/), [IGVFFI5859ORLB](/sequence-files/IGVFFI5859ORLB/), [IGVFFI1570GPJB](/sequence-files/IGVFFI1570GPJB/) 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/IGVFDS6085VVNC/"
},
{
"category": "mismatched status",
"detail": "Released in vitro system [IGVFSM3390LNPT](/in-vitro-systems/IGVFSM3390LNPT/) 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/IGVFSM3390LNPT/"
},
{
"category": "missing publication",
"detail": "In vitro system [IGVFSM3390LNPT](/in-vitro-systems/IGVFSM3390LNPT/) 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/IGVFSM3390LNPT/"
}
],
"NOT_COMPLIANT": [
{
"category": "missing sequence specification",
"detail": "Measurement set [IGVFDS6085VVNC](/measurement-sets/IGVFDS6085VVNC/) has sequence file(s): [IGVFFI9152EMSR](/sequence-files/IGVFFI9152EMSR/), [IGVFFI9927UHCN](/sequence-files/IGVFFI9927UHCN/), [IGVFFI0594ANPV](/sequence-files/IGVFFI0594ANPV/), [IGVFFI2437ZQEH](/sequence-files/IGVFFI2437ZQEH/), [IGVFFI5430ZDLE](/sequence-files/IGVFFI5430ZDLE/), [IGVFFI6834BFYY](/sequence-files/IGVFFI6834BFYY/), [IGVFFI5859ORLB](/sequence-files/IGVFFI5859ORLB/), [IGVFFI1570GPJB](/sequence-files/IGVFFI1570GPJB/) which do not have a `seqspec_document`. Sequence files in a file set associated with non-single cell data are expected to link to a sequence specification document.",
"level": 50,
"level_name": "NOT_COMPLIANT",
"name": "audit_missing_seqspec",
"path": "/measurement-sets/IGVFDS6085VVNC/"
}
],
"WARNING": [
{
"category": "missing auxiliary set",
"detail": "Measurement set [IGVFDS6085VVNC](/measurement-sets/IGVFDS6085VVNC/) 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/IGVFDS6085VVNC/"
}
]
},
"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/IGVFDS9477ARWI/",
"accession": "IGVFDS9477ARWI",
"aliases": [
"jesse-engreitz:220829_8merInsertion-Jurkat_NoStimulation-Amp_PPIF_promoter-Jurkat-PE2_Exp1_NegControl_AmpliconSequencing",
"jesse-engreitz:220829_8merInsertion-Jurkat_Stimulation-Amp_PPIF_promoter-Jurkat-PE2_Exp1_NegControl_AmpliconSequencing"
],
"status": "released"
}
],
"control_for": [],
"creation_timestamp": "2023-11-30T22:47:53.572274+00:00",
"data_use_limitation_summaries": [
"no certificate"
],
"donors": [
{
"@id": "/human-donors/IGVFDO1080XFGV/",
"accession": "IGVFDO1080XFGV",
"aliases": [
"igvf:donor_of_Jurkat"
],
"sex": "male",
"status": "released",
"taxa": "Homo sapiens"
}
],
"externally_hosted": false,
"file_set_type": "experimental data",
"files": [
{
"@id": "/sequence-files/IGVFFI9152EMSR/",
"accession": "IGVFFI9152EMSR",
"aliases": [
"jesse-engreitz:220829_8merInsertion-Jurkat_Stimulation-Amp_PPIF_promoter-BioRep1-FFrep2-BinA-PCRrep1_I2"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2023-12-05T19:56:51.493817+00:00",
"file_format": "fastq",
"file_size": 3173572,
"href": "/sequence-files/IGVFFI9152EMSR/@@download/IGVFFI9152EMSR.fastq.gz",
"md5sum": "30298b98b02d2e77c05e861d6cc57d99",
"s3_uri": "s3://igvf-files/2023/12/05/1e9c42da-5485-47ba-9dc1-0df1ff1cbf4e/IGVFFI9152EMSR.fastq.gz",
"sequencing_platform": {
"@id": "/platform-terms/EFO_0008566/",
"status": "released",
"term_name": "Illumina NextSeq 550"
},
"status": "released",
"submitted_file_name": "220829_pPPIF_JurkatVFF-Jurkat-PE2A-BFP-pPPIF-Amp_pPPIF2_S13-BioRep1-FFRep2-BinA-PCRrep1_S120_I2_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI9927UHCN/",
"accession": "IGVFFI9927UHCN",
"aliases": [
"jesse-engreitz:220829_8merInsertion-Jurkat_Stimulation-Amp_PPIF_promoter-BioRep1-FFrep2-BinA-PCRrep2_R1"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2023-12-05T20:04:59.999740+00:00",
"file_format": "fastq",
"file_size": 7476970,
"href": "/sequence-files/IGVFFI9927UHCN/@@download/IGVFFI9927UHCN.fastq.gz",
"md5sum": "8efb272c30d7cc90b422138ba099689e",
"s3_uri": "s3://igvf-files/2023/12/05/e5d8b9fd-655d-4354-8ea8-ae4be9e053e7/IGVFFI9927UHCN.fastq.gz",
"sequencing_platform": {
"@id": "/platform-terms/EFO_0008566/",
"status": "released",
"term_name": "Illumina NextSeq 550"
},
"status": "released",
"submitted_file_name": "220829_pPPIF_JurkatVFF-Jurkat-PE2A-BFP-pPPIF-Amp_pPPIF2_S13-BioRep1-FFRep2-BinA-PCRrep2_S177_R1_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI0594ANPV/",
"accession": "IGVFFI0594ANPV",
"aliases": [
"jesse-engreitz:220829_8merInsertion-Jurkat_Stimulation-Amp_PPIF_promoter-BioRep1-FFrep2-BinA-PCRrep1_I1"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2023-12-05T19:48:43.752934+00:00",
"file_format": "fastq",
"file_size": 3221415,
"href": "/sequence-files/IGVFFI0594ANPV/@@download/IGVFFI0594ANPV.fastq.gz",
"md5sum": "75110f5604c732cc53e2227fc1a9addf",
"s3_uri": "s3://igvf-files/2023/12/05/af08fdac-f2c0-4b27-a5c2-3efe573fee29/IGVFFI0594ANPV.fastq.gz",
"sequencing_platform": {
"@id": "/platform-terms/EFO_0008566/",
"status": "released",
"term_name": "Illumina NextSeq 550"
},
"status": "released",
"submitted_file_name": "220829_pPPIF_JurkatVFF-Jurkat-PE2A-BFP-pPPIF-Amp_pPPIF2_S13-BioRep1-FFRep2-BinA-PCRrep1_S120_I1_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI2437ZQEH/",
"accession": "IGVFFI2437ZQEH",
"aliases": [
"jesse-engreitz:220829_8merInsertion-Jurkat_Stimulation-Amp_PPIF_promoter-BioRep1-FFrep2-BinA-PCRrep2_R2"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2023-12-05T20:13:19.222232+00:00",
"file_format": "fastq",
"file_size": 13580488,
"href": "/sequence-files/IGVFFI2437ZQEH/@@download/IGVFFI2437ZQEH.fastq.gz",
"md5sum": "9bd440f28bb9d9ebd5f63013cde42945",
"s3_uri": "s3://igvf-files/2023/12/05/a8ec13d5-b358-463b-bab1-690267c2c21d/IGVFFI2437ZQEH.fastq.gz",
"sequencing_platform": {
"@id": "/platform-terms/EFO_0008566/",
"status": "released",
"term_name": "Illumina NextSeq 550"
},
"status": "released",
"submitted_file_name": "220829_pPPIF_JurkatVFF-Jurkat-PE2A-BFP-pPPIF-Amp_pPPIF2_S13-BioRep1-FFRep2-BinA-PCRrep2_S177_R2_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI5430ZDLE/",
"accession": "IGVFFI5430ZDLE",
"aliases": [
"jesse-engreitz:220829_8merInsertion-Jurkat_Stimulation-Amp_PPIF_promoter-BioRep1-FFrep2-BinA-PCRrep1_R2"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2023-12-05T19:40:08.506716+00:00",
"file_format": "fastq",
"file_size": 13994694,
"href": "/sequence-files/IGVFFI5430ZDLE/@@download/IGVFFI5430ZDLE.fastq.gz",
"md5sum": "40195f2e63294e0f491a94ef064cb453",
"s3_uri": "s3://igvf-files/2023/12/05/a337b3d9-59a9-4b99-bc3c-7c1a8eb92c1c/IGVFFI5430ZDLE.fastq.gz",
"sequencing_platform": {
"@id": "/platform-terms/EFO_0008566/",
"status": "released",
"term_name": "Illumina NextSeq 550"
},
"status": "released",
"submitted_file_name": "220829_pPPIF_JurkatVFF-Jurkat-PE2A-BFP-pPPIF-Amp_pPPIF2_S13-BioRep1-FFRep2-BinA-PCRrep1_S120_R2_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI6834BFYY/",
"accession": "IGVFFI6834BFYY",
"aliases": [
"jesse-engreitz:220829_8merInsertion-Jurkat_Stimulation-Amp_PPIF_promoter-BioRep1-FFrep2-BinA-PCRrep1_R1"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2023-12-05T19:31:46.429954+00:00",
"file_format": "fastq",
"file_size": 7644131,
"href": "/sequence-files/IGVFFI6834BFYY/@@download/IGVFFI6834BFYY.fastq.gz",
"md5sum": "e2baad86e1f3a6f1c923e2bb7be1889b",
"s3_uri": "s3://igvf-files/2023/12/05/ff4aec68-8b67-4284-8add-ac0b7a7f85e4/IGVFFI6834BFYY.fastq.gz",
"sequencing_platform": {
"@id": "/platform-terms/EFO_0008566/",
"status": "released",
"term_name": "Illumina NextSeq 550"
},
"status": "released",
"submitted_file_name": "220829_pPPIF_JurkatVFF-Jurkat-PE2A-BFP-pPPIF-Amp_pPPIF2_S13-BioRep1-FFRep2-BinA-PCRrep1_S120_R1_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI5859ORLB/",
"accession": "IGVFFI5859ORLB",
"aliases": [
"jesse-engreitz:220829_8merInsertion-Jurkat_Stimulation-Amp_PPIF_promoter-BioRep1-FFrep2-BinA-PCRrep2_I1"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2023-12-05T20:21:48.903649+00:00",
"file_format": "fastq",
"file_size": 3095924,
"href": "/sequence-files/IGVFFI5859ORLB/@@download/IGVFFI5859ORLB.fastq.gz",
"md5sum": "c3152240ee64885dda4e54b03a3ee5e5",
"s3_uri": "s3://igvf-files/2023/12/05/4aa6bbf2-c429-434a-bbdc-97954f90fa86/IGVFFI5859ORLB.fastq.gz",
"sequencing_platform": {
"@id": "/platform-terms/EFO_0008566/",
"status": "released",
"term_name": "Illumina NextSeq 550"
},
"status": "released",
"submitted_file_name": "220829_pPPIF_JurkatVFF-Jurkat-PE2A-BFP-pPPIF-Amp_pPPIF2_S13-BioRep1-FFRep2-BinA-PCRrep2_S177_I1_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI1570GPJB/",
"accession": "IGVFFI1570GPJB",
"aliases": [
"jesse-engreitz:220829_8merInsertion-Jurkat_Stimulation-Amp_PPIF_promoter-BioRep1-FFrep2-BinA-PCRrep2_I2"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2023-12-05T20:30:09.191247+00:00",
"file_format": "fastq",
"file_size": 3087093,
"href": "/sequence-files/IGVFFI1570GPJB/@@download/IGVFFI1570GPJB.fastq.gz",
"md5sum": "4eeba787d8fd87e9c854a0dbaf5f5ddd",
"s3_uri": "s3://igvf-files/2023/12/05/91fc2c08-ce89-4c99-b402-179d283208f3/IGVFFI1570GPJB.fastq.gz",
"sequencing_platform": {
"@id": "/platform-terms/EFO_0008566/",
"status": "released",
"term_name": "Illumina NextSeq 550"
},
"status": "released",
"submitted_file_name": "220829_pPPIF_JurkatVFF-Jurkat-PE2A-BFP-pPPIF-Amp_pPPIF2_S13-BioRep1-FFRep2-BinA-PCRrep2_S177_I2_001.fastq.gz",
"upload_status": "validated"
}
],
"input_for": [
"/analysis-sets/IGVFDS1863TJOE/"
],
"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": "2023-12-20T23:10:29.448401+00:00",
"samples": [
{
"@id": "/in-vitro-systems/IGVFSM3390LNPT/",
"@type": [
"InVitroSystem",
"Biosample",
"Sample",
"Item"
],
"accession": "IGVFSM3390LNPT",
"aliases": [
"jesse-engreitz:220829_8merInsertion-Jurkat_Stimulation-Amp_PPIF_promoter-BioRep1-FFrep2-BinA"
],
"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_0002796/",
"@type": [
"SampleTerm",
"OntologyTerm",
"Item"
],
"aliases": [
"igvf:Jurkat"
],
"status": "released",
"summary": "Jurkat",
"term_name": "Jurkat"
}
],
"status": "released",
"summary": "Homo sapiens (male) Jurkat cell line (sorting details: FACS bin for 0-10% expression of PPIF) treated with 100 ng/mL phorbol 13-acetate 12-myristate for 4 hours, 5 μg/mL T-cell surface glycoprotein CD3 gamma chain for 4 hours, modified with CRISPR prime editing Sp-nCas9-M-MLV RT (PE2), transduced (lentivirus) with a guide library",
"taxa": "Homo sapiens",
"treatments": [
{
"@id": "/treatments/df02c0d4-f796-4f77-bfbc-388cdbfcc615/",
"purpose": "stimulation",
"status": "released",
"summary": "Treatment of 5 μg/mL T-cell surface glycoprotein CD3 gamma chain for 4 hours",
"treatment_term_name": "T-cell surface glycoprotein CD3 gamma chain",
"treatment_type": "protein"
},
{
"@id": "/treatments/42b3c61d-38de-4bd2-bb39-33c125a417cb/",
"purpose": "stimulation",
"status": "released",
"summary": "Treatment of 100 ng/mL phorbol 13-acetate 12-myristate for 4 hours",
"treatment_term_name": "phorbol 13-acetate 12-myristate",
"treatment_type": "chemical"
}
]
}
],
"schema_version": "26",
"status": "released",
"submitted_by": {
"@id": "/users/f9e7cd82-a407-4a20-89ee-f4dc668b0cbe/",
"title": "Michael Montgomery"
},
"submitted_files_timestamp": "2023-12-05T19:31:46.429954+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": "0b677c3a-2dbf-4a37-afe2-fd1e74bab089"
}