{
"@context": "/terms/",
"@id": "/measurement-sets/IGVFDS3682SXGQ/",
"@type": [
"MeasurementSet",
"FileSet",
"Item"
],
"accession": "IGVFDS3682SXGQ",
"aliases": [
"jesse-engreitz:220829_8merInsertion-Jurkat_NoStimulation-Amp_PPIF_promoter-BioRep3-FFrep2-BinA_AmpliconSequencing"
],
"assay_term": {
"@id": "/assay-terms/OBI_0003661/",
"status": "released",
"term_name": "in vitro CRISPR screen using flow cytometry"
},
"audit": {
"INTERNAL_ACTION": [
{
"category": "missing sequencing kit",
"detail": "Measurement set [IGVFDS3682SXGQ](/measurement-sets/IGVFDS3682SXGQ/) has sequence file(s) [IGVFFI6988USNI](/sequence-files/IGVFFI6988USNI/), [IGVFFI6030MOQF](/sequence-files/IGVFFI6030MOQF/), [IGVFFI0853THFP](/sequence-files/IGVFFI0853THFP/), [IGVFFI5169USSN](/sequence-files/IGVFFI5169USSN/), [IGVFFI0863NJVR](/sequence-files/IGVFFI0863NJVR/), [IGVFFI7675FCTZ](/sequence-files/IGVFFI7675FCTZ/), [IGVFFI5035ZVEY](/sequence-files/IGVFFI5035ZVEY/), [IGVFFI3788ZAUZ](/sequence-files/IGVFFI3788ZAUZ/) which lack specification of a `sequencing_kit`. Sequence files should specify a sequencing kit.",
"level": 30,
"level_name": "INTERNAL_ACTION",
"name": "audit_inconsistent_sequencing_kit",
"path": "/measurement-sets/IGVFDS3682SXGQ/"
},
{
"category": "missing sequence specification",
"detail": "Measurement set [IGVFDS3682SXGQ](/measurement-sets/IGVFDS3682SXGQ/) has sequence file(s): [IGVFFI6988USNI](/sequence-files/IGVFFI6988USNI/), [IGVFFI6030MOQF](/sequence-files/IGVFFI6030MOQF/), [IGVFFI0853THFP](/sequence-files/IGVFFI0853THFP/), [IGVFFI5169USSN](/sequence-files/IGVFFI5169USSN/), [IGVFFI0863NJVR](/sequence-files/IGVFFI0863NJVR/), [IGVFFI7675FCTZ](/sequence-files/IGVFFI7675FCTZ/), [IGVFFI5035ZVEY](/sequence-files/IGVFFI5035ZVEY/), [IGVFFI3788ZAUZ](/sequence-files/IGVFFI3788ZAUZ/) which do not have any `seqspecs`. Sequence files in a file set are expected to link to a sequence specification file.",
"level": 30,
"level_name": "INTERNAL_ACTION",
"name": "audit_missing_seqspec",
"path": "/measurement-sets/IGVFDS3682SXGQ/"
},
{
"category": "mismatched status",
"detail": "Released in vitro system [IGVFSM5747TVXR](/in-vitro-systems/IGVFSM5747TVXR/) 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/IGVFSM5747TVXR/"
}
],
"WARNING": [
{
"category": "missing auxiliary set",
"detail": "Measurement set [IGVFDS3682SXGQ](/measurement-sets/IGVFDS3682SXGQ/) 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/IGVFDS3682SXGQ/"
}
]
},
"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"
},
"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": "2023-11-30T22:47:37.830121+00:00",
"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": [
{
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"accession": "IGVFFI6988USNI",
"aliases": [
"jesse-engreitz:220829_8merInsertion-Jurkat_NoStimulation-Amp_PPIF_promoter-BioRep3-FFrep2-BinA-PCRrep1_R2"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2023-12-05T18:57:49.453042+00:00",
"file_format": "fastq",
"file_size": 15386878,
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"s3_uri": "s3://igvf-files/2023/12/05/d4469c08-3566-4ae3-ae9f-a52abe356946/IGVFFI6988USNI.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_pPPIF_S8-BioRep3-FFRep2-BinA-PCRrep1_S36_R2_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI6030MOQF/",
"accession": "IGVFFI6030MOQF",
"aliases": [
"jesse-engreitz:220829_8merInsertion-Jurkat_NoStimulation-Amp_PPIF_promoter-BioRep3-FFrep2-BinA-PCRrep2_I2"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2023-12-05T19:29:34.240884+00:00",
"file_format": "fastq",
"file_size": 3263486,
"href": "/sequence-files/IGVFFI6030MOQF/@@download/IGVFFI6030MOQF.fastq.gz",
"s3_uri": "s3://igvf-files/2023/12/05/66928299-1cc5-4e76-ba41-0c70cd64ee10/IGVFFI6030MOQF.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_pPPIF_S8-BioRep3-FFRep2-BinA-PCRrep2_S92_I2_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI0853THFP/",
"accession": "IGVFFI0853THFP",
"aliases": [
"jesse-engreitz:220829_8merInsertion-Jurkat_NoStimulation-Amp_PPIF_promoter-BioRep3-FFrep2-BinA-PCRrep1_I2"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2023-12-05T19:23:19.565715+00:00",
"file_format": "fastq",
"file_size": 3428300,
"href": "/sequence-files/IGVFFI0853THFP/@@download/IGVFFI0853THFP.fastq.gz",
"s3_uri": "s3://igvf-files/2023/12/05/8f78a782-e59f-4515-8947-541c8328ac28/IGVFFI0853THFP.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_pPPIF_S8-BioRep3-FFRep2-BinA-PCRrep1_S36_I2_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI5169USSN/",
"accession": "IGVFFI5169USSN",
"aliases": [
"jesse-engreitz:220829_8merInsertion-Jurkat_NoStimulation-Amp_PPIF_promoter-BioRep3-FFrep2-BinA-PCRrep2_R2"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2023-12-05T19:04:26.908638+00:00",
"file_format": "fastq",
"file_size": 14730223,
"href": "/sequence-files/IGVFFI5169USSN/@@download/IGVFFI5169USSN.fastq.gz",
"s3_uri": "s3://igvf-files/2023/12/05/4ca8e5c1-52c9-45d5-b209-a5bf2989dea4/IGVFFI5169USSN.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_pPPIF_S8-BioRep3-FFRep2-BinA-PCRrep2_S92_R2_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI0863NJVR/",
"accession": "IGVFFI0863NJVR",
"aliases": [
"jesse-engreitz:220829_8merInsertion-Jurkat_NoStimulation-Amp_PPIF_promoter-BioRep3-FFrep2-BinA-PCRrep1_R1"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2023-12-05T18:45:01.170543+00:00",
"file_format": "fastq",
"file_size": 8440285,
"href": "/sequence-files/IGVFFI0863NJVR/@@download/IGVFFI0863NJVR.fastq.gz",
"s3_uri": "s3://igvf-files/2023/12/05/aa13d47a-c885-4b19-bd15-30397244aa2b/IGVFFI0863NJVR.fastq.gz",
"sequencing_platform": {
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"status": "released",
"term_name": "Illumina NextSeq 550"
},
"status": "released",
"submitted_file_name": "220829_pPPIF_JurkatVFF-Jurkat-PE2A-BFP-pPPIF-Amp_pPPIF_S8-BioRep3-FFRep2-BinA-PCRrep1_S36_R1_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI7675FCTZ/",
"accession": "IGVFFI7675FCTZ",
"aliases": [
"jesse-engreitz:220829_8merInsertion-Jurkat_NoStimulation-Amp_PPIF_promoter-BioRep3-FFrep2-BinA-PCRrep2_I1"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2023-12-05T19:16:58.959646+00:00",
"file_format": "fastq",
"file_size": 3626241,
"href": "/sequence-files/IGVFFI7675FCTZ/@@download/IGVFFI7675FCTZ.fastq.gz",
"s3_uri": "s3://igvf-files/2023/12/05/a1540ccd-b704-454a-962a-243953dd1240/IGVFFI7675FCTZ.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_pPPIF_S8-BioRep3-FFRep2-BinA-PCRrep2_S92_I1_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI5035ZVEY/",
"accession": "IGVFFI5035ZVEY",
"aliases": [
"jesse-engreitz:220829_8merInsertion-Jurkat_NoStimulation-Amp_PPIF_promoter-BioRep3-FFrep2-BinA-PCRrep2_R1"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2023-12-05T18:51:19.398621+00:00",
"file_format": "fastq",
"file_size": 8127034,
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"sequencing_platform": {
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"status": "released",
"term_name": "Illumina NextSeq 550"
},
"status": "released",
"submitted_file_name": "220829_pPPIF_JurkatVFF-Jurkat-PE2A-BFP-pPPIF-Amp_pPPIF_S8-BioRep3-FFRep2-BinA-PCRrep2_S92_R1_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI3788ZAUZ/",
"accession": "IGVFFI3788ZAUZ",
"aliases": [
"jesse-engreitz:220829_8merInsertion-Jurkat_NoStimulation-Amp_PPIF_promoter-BioRep3-FFrep2-BinA-PCRrep1_I1"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2023-12-05T19:10:43.516624+00:00",
"file_format": "fastq",
"file_size": 3556400,
"href": "/sequence-files/IGVFFI3788ZAUZ/@@download/IGVFFI3788ZAUZ.fastq.gz",
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"sequencing_platform": {
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"status": "released",
"term_name": "Illumina NextSeq 550"
},
"status": "released",
"submitted_file_name": "220829_pPPIF_JurkatVFF-Jurkat-PE2A-BFP-pPPIF-Amp_pPPIF_S8-BioRep3-FFRep2-BinA-PCRrep1_S36_I1_001.fastq.gz",
"upload_status": "validated"
}
],
"input_for": [
"/analysis-sets/IGVFDS9162RHFP/"
],
"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": "2023-12-20T23:04:53.896632+00:00",
"samples": [
{
"@id": "/in-vitro-systems/IGVFSM5747TVXR/",
"@type": [
"InVitroSystem",
"Biosample",
"Sample",
"Item"
],
"accession": "IGVFSM5747TVXR",
"aliases": [
"jesse-engreitz:220829_8merInsertion-Jurkat_NoStimulation-Amp_PPIF_promoter-BioRep3-FFrep2-BinA"
],
"classifications": [
"cell line"
],
"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"
}
],
"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": "Jurkat cell line, male, Homo sapiens (sorting details: FACS bin for 0-10% expression of PPIF) modified with CRISPR prime editing Sp-nCas9-M-MLV RT (PE2), transfected with a guide library",
"taxa": "Homo sapiens"
}
],
"schema_version": "23",
"status": "released",
"submitted_by": {
"@id": "/users/f9e7cd82-a407-4a20-89ee-f4dc668b0cbe/",
"title": "Michael Montgomery"
},
"submitted_files_timestamp": "2023-12-05T18:45:01.170543+00:00",
"summary": "CRISPR prime editing Variant-EFFECTS 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": [
"rotamase F",
"CYP3",
"cyclophilin F",
"mitochondrial cyclophilin",
"peptidyl-prolyl cis-trans isomerase, mitochondrial",
"CypD",
"Cyp-D",
"cyclophilin 3",
"cyclophilin D",
"CyP-M",
"peptidyl-prolyl cis-trans isomerase F, mitochondrial",
"PPIase F"
]
}
],
"uuid": "e6eca4e8-ab23-4213-b327-83d9151dd4b5"
}