{
"@context": "/terms/",
"@id": "/measurement-sets/IGVFDS5223WASR/",
"@type": [
"MeasurementSet",
"FileSet",
"Item"
],
"accession": "IGVFDS5223WASR",
"aliases": [
"jesse-engreitz:220829_8merInsertion-Jurkat_NoStimulation-Amp_PPIF_promoter-BioRep2-FFrep2-BinB_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 [IGVFDS5223WASR](/measurement-sets/IGVFDS5223WASR/) has sequence file(s) [IGVFFI6397FFML](/sequence-files/IGVFFI6397FFML/), [IGVFFI9087VKGR](/sequence-files/IGVFFI9087VKGR/), [IGVFFI8230BLDT](/sequence-files/IGVFFI8230BLDT/), [IGVFFI4851HHXB](/sequence-files/IGVFFI4851HHXB/), [IGVFFI6553PABF](/sequence-files/IGVFFI6553PABF/), [IGVFFI0101EAJU](/sequence-files/IGVFFI0101EAJU/), [IGVFFI4121SEAR](/sequence-files/IGVFFI4121SEAR/), [IGVFFI1182GWWX](/sequence-files/IGVFFI1182GWWX/) 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/IGVFDS5223WASR/"
},
{
"category": "missing sequence specification",
"detail": "Measurement set [IGVFDS5223WASR](/measurement-sets/IGVFDS5223WASR/) has sequence file(s): [IGVFFI6397FFML](/sequence-files/IGVFFI6397FFML/), [IGVFFI9087VKGR](/sequence-files/IGVFFI9087VKGR/), [IGVFFI8230BLDT](/sequence-files/IGVFFI8230BLDT/), [IGVFFI4851HHXB](/sequence-files/IGVFFI4851HHXB/), [IGVFFI6553PABF](/sequence-files/IGVFFI6553PABF/), [IGVFFI0101EAJU](/sequence-files/IGVFFI0101EAJU/), [IGVFFI4121SEAR](/sequence-files/IGVFFI4121SEAR/), [IGVFFI1182GWWX](/sequence-files/IGVFFI1182GWWX/) 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/IGVFDS5223WASR/"
},
{
"category": "mismatched status",
"detail": "Released in vitro system [IGVFSM0345RIFG](/in-vitro-systems/IGVFSM0345RIFG/) 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/IGVFSM0345RIFG/"
}
],
"WARNING": [
{
"category": "missing auxiliary set",
"detail": "Measurement set [IGVFDS5223WASR](/measurement-sets/IGVFDS5223WASR/) 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/IGVFDS5223WASR/"
}
]
},
"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": "2023-11-30T22:47:24.870442+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": [
{
"@id": "/sequence-files/IGVFFI6397FFML/",
"accession": "IGVFFI6397FFML",
"aliases": [
"jesse-engreitz:220829_8merInsertion-Jurkat_NoStimulation-Amp_PPIF_promoter-BioRep2-FFrep2-BinB-PCRrep1_I1"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2023-12-05T19:08:50.317927+00:00",
"file_format": "fastq",
"file_size": 3370854,
"href": "/sequence-files/IGVFFI6397FFML/@@download/IGVFFI6397FFML.fastq.gz",
"s3_uri": "s3://igvf-files/2023/12/05/2d634653-9cdb-4d93-8072-4a7f6e30f18a/IGVFFI6397FFML.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_S6-BioRep2-FFRep2-BinB-PCRrep1_S23_I1_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI9087VKGR/",
"accession": "IGVFFI9087VKGR",
"aliases": [
"jesse-engreitz:220829_8merInsertion-Jurkat_NoStimulation-Amp_PPIF_promoter-BioRep2-FFrep2-BinB-PCRrep1_R2"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2023-12-05T18:55:50.591771+00:00",
"file_format": "fastq",
"file_size": 13972672,
"href": "/sequence-files/IGVFFI9087VKGR/@@download/IGVFFI9087VKGR.fastq.gz",
"s3_uri": "s3://igvf-files/2023/12/05/1b36489c-9f29-4d4e-b4cd-3d89a37119ae/IGVFFI9087VKGR.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_S6-BioRep2-FFRep2-BinB-PCRrep1_S23_R2_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI8230BLDT/",
"accession": "IGVFFI8230BLDT",
"aliases": [
"jesse-engreitz:220829_8merInsertion-Jurkat_NoStimulation-Amp_PPIF_promoter-BioRep2-FFrep2-BinB-PCRrep2_R2"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2023-12-05T19:02:28.561337+00:00",
"file_format": "fastq",
"file_size": 14271145,
"href": "/sequence-files/IGVFFI8230BLDT/@@download/IGVFFI8230BLDT.fastq.gz",
"s3_uri": "s3://igvf-files/2023/12/05/db5aa733-014a-443c-add3-42c92719832f/IGVFFI8230BLDT.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_S6-BioRep2-FFRep2-BinB-PCRrep2_S79_R2_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI4851HHXB/",
"accession": "IGVFFI4851HHXB",
"aliases": [
"jesse-engreitz:220829_8merInsertion-Jurkat_NoStimulation-Amp_PPIF_promoter-BioRep2-FFrep2-BinB-PCRrep2_R1"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2023-12-05T18:49:25.328435+00:00",
"file_format": "fastq",
"file_size": 7857821,
"href": "/sequence-files/IGVFFI4851HHXB/@@download/IGVFFI4851HHXB.fastq.gz",
"s3_uri": "s3://igvf-files/2023/12/05/81fd1df6-8ec1-40c2-9814-4598095f14d6/IGVFFI4851HHXB.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_S6-BioRep2-FFRep2-BinB-PCRrep2_S79_R1_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI6553PABF/",
"accession": "IGVFFI6553PABF",
"aliases": [
"jesse-engreitz:220829_8merInsertion-Jurkat_NoStimulation-Amp_PPIF_promoter-BioRep2-FFrep2-BinB-PCRrep2_I1"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2023-12-05T19:15:05.518631+00:00",
"file_format": "fastq",
"file_size": 3328076,
"href": "/sequence-files/IGVFFI6553PABF/@@download/IGVFFI6553PABF.fastq.gz",
"s3_uri": "s3://igvf-files/2023/12/05/41777cee-95eb-4514-b822-0d4aa1a98861/IGVFFI6553PABF.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_S6-BioRep2-FFRep2-BinB-PCRrep2_S79_I1_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI0101EAJU/",
"accession": "IGVFFI0101EAJU",
"aliases": [
"jesse-engreitz:220829_8merInsertion-Jurkat_NoStimulation-Amp_PPIF_promoter-BioRep2-FFrep2-BinB-PCRrep1_R1"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2023-12-05T18:43:06.670628+00:00",
"file_format": "fastq",
"file_size": 7713078,
"href": "/sequence-files/IGVFFI0101EAJU/@@download/IGVFFI0101EAJU.fastq.gz",
"s3_uri": "s3://igvf-files/2023/12/05/8af29a29-5e38-4b55-a8dd-735405e21a8f/IGVFFI0101EAJU.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_S6-BioRep2-FFRep2-BinB-PCRrep1_S23_R1_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI4121SEAR/",
"accession": "IGVFFI4121SEAR",
"aliases": [
"jesse-engreitz:220829_8merInsertion-Jurkat_NoStimulation-Amp_PPIF_promoter-BioRep2-FFrep2-BinB-PCRrep1_I2"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2023-12-05T19:21:22.169488+00:00",
"file_format": "fastq",
"file_size": 3119775,
"href": "/sequence-files/IGVFFI4121SEAR/@@download/IGVFFI4121SEAR.fastq.gz",
"s3_uri": "s3://igvf-files/2023/12/05/1dc48d8c-4862-4a62-bfed-402ed867aba8/IGVFFI4121SEAR.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_S6-BioRep2-FFRep2-BinB-PCRrep1_S23_I2_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI1182GWWX/",
"accession": "IGVFFI1182GWWX",
"aliases": [
"jesse-engreitz:220829_8merInsertion-Jurkat_NoStimulation-Amp_PPIF_promoter-BioRep2-FFrep2-BinB-PCRrep2_I2"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2023-12-05T19:27:41.328002+00:00",
"file_format": "fastq",
"file_size": 3176582,
"href": "/sequence-files/IGVFFI1182GWWX/@@download/IGVFFI1182GWWX.fastq.gz",
"s3_uri": "s3://igvf-files/2023/12/05/e90dbe04-ed29-4588-b5cc-f60a995b5124/IGVFFI1182GWWX.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_S6-BioRep2-FFRep2-BinB-PCRrep2_S79_I2_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": "2023-12-20T23:03:43.044723+00:00",
"samples": [
{
"@id": "/in-vitro-systems/IGVFSM0345RIFG/",
"@type": [
"InVitroSystem",
"Biosample",
"Sample",
"Item"
],
"accession": "IGVFSM0345RIFG",
"aliases": [
"jesse-engreitz:220829_8merInsertion-Jurkat_NoStimulation-Amp_PPIF_promoter-BioRep2-FFrep2-BinB"
],
"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 11-20% 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": "2023-12-05T18:43:06.670628+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": "0ec6ae98-2e7b-49d2-ac83-0e0f8db02edf"
}