{
"@context": "/terms/",
"@id": "/measurement-sets/IGVFDS0667KDIQ/",
"@type": [
"MeasurementSet",
"FileSet",
"Item"
],
"accession": "IGVFDS0667KDIQ",
"aliases": [
"jesse-engreitz:220829_8merInsertion-Jurkat_NoStimulation-Amp_PPIF_promoter-BioRep1-FFrep2-BinE_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 [IGVFDS0667KDIQ](/measurement-sets/IGVFDS0667KDIQ/) has sequence file(s) [IGVFFI4718BVCV](/sequence-files/IGVFFI4718BVCV/), [IGVFFI9778DBDT](/sequence-files/IGVFFI9778DBDT/), [IGVFFI5906BPMV](/sequence-files/IGVFFI5906BPMV/), [IGVFFI9800CRJB](/sequence-files/IGVFFI9800CRJB/), [IGVFFI7455QOMR](/sequence-files/IGVFFI7455QOMR/), [IGVFFI6164WJVT](/sequence-files/IGVFFI6164WJVT/), [IGVFFI9886JCGH](/sequence-files/IGVFFI9886JCGH/), [IGVFFI8365CSFD](/sequence-files/IGVFFI8365CSFD/) 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/IGVFDS0667KDIQ/"
},
{
"category": "missing sequence specification",
"detail": "Measurement set [IGVFDS0667KDIQ](/measurement-sets/IGVFDS0667KDIQ/) has sequence file(s): [IGVFFI4718BVCV](/sequence-files/IGVFFI4718BVCV/), [IGVFFI9778DBDT](/sequence-files/IGVFFI9778DBDT/), [IGVFFI5906BPMV](/sequence-files/IGVFFI5906BPMV/), [IGVFFI9800CRJB](/sequence-files/IGVFFI9800CRJB/), [IGVFFI7455QOMR](/sequence-files/IGVFFI7455QOMR/), [IGVFFI6164WJVT](/sequence-files/IGVFFI6164WJVT/), [IGVFFI9886JCGH](/sequence-files/IGVFFI9886JCGH/), [IGVFFI8365CSFD](/sequence-files/IGVFFI8365CSFD/) 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/IGVFDS0667KDIQ/"
},
{
"category": "mismatched status",
"detail": "Released in vitro system [IGVFSM0553VHCD](/in-vitro-systems/IGVFSM0553VHCD/) 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/IGVFSM0553VHCD/"
}
],
"WARNING": [
{
"category": "missing auxiliary set",
"detail": "Measurement set [IGVFDS0667KDIQ](/measurement-sets/IGVFDS0667KDIQ/) 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/IGVFDS0667KDIQ/"
}
]
},
"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": "2023-11-30T22:47:13.068776+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/IGVFFI4718BVCV/",
"accession": "IGVFFI4718BVCV",
"aliases": [
"jesse-engreitz:220829_8merInsertion-Jurkat_NoStimulation-Amp_PPIF_promoter-BioRep1-FFrep2-BinE-PCRrep2_I1"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2023-12-05T19:13:29.632768+00:00",
"file_format": "fastq",
"file_size": 3228531,
"href": "/sequence-files/IGVFFI4718BVCV/@@download/IGVFFI4718BVCV.fastq.gz",
"s3_uri": "s3://igvf-files/2023/12/05/47ce110f-08f9-405a-be8d-57b79a2f0e16/IGVFFI4718BVCV.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_S3-BioRep1-FFRep2-BinE-PCRrep2_S68_I1_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI9778DBDT/",
"accession": "IGVFFI9778DBDT",
"aliases": [
"jesse-engreitz:220829_8merInsertion-Jurkat_NoStimulation-Amp_PPIF_promoter-BioRep1-FFrep2-BinE-PCRrep1_R1"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2023-12-05T18:41:30.149578+00:00",
"file_format": "fastq",
"file_size": 1720142,
"href": "/sequence-files/IGVFFI9778DBDT/@@download/IGVFFI9778DBDT.fastq.gz",
"s3_uri": "s3://igvf-files/2023/12/05/a6d5d780-f4cb-4ccb-bbf6-fffa1eed221b/IGVFFI9778DBDT.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_S3-BioRep1-FFRep2-BinE-PCRrep1_S12_R1_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI5906BPMV/",
"accession": "IGVFFI5906BPMV",
"aliases": [
"jesse-engreitz:220829_8merInsertion-Jurkat_NoStimulation-Amp_PPIF_promoter-BioRep1-FFrep2-BinE-PCRrep2_R2"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2023-12-05T19:00:46.704743+00:00",
"file_format": "fastq",
"file_size": 14280008,
"href": "/sequence-files/IGVFFI5906BPMV/@@download/IGVFFI5906BPMV.fastq.gz",
"s3_uri": "s3://igvf-files/2023/12/05/37182e0b-8f82-47f2-a9f1-c1f73315826d/IGVFFI5906BPMV.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_S3-BioRep1-FFRep2-BinE-PCRrep2_S68_R2_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI9800CRJB/",
"accession": "IGVFFI9800CRJB",
"aliases": [
"jesse-engreitz:220829_8merInsertion-Jurkat_NoStimulation-Amp_PPIF_promoter-BioRep1-FFrep2-BinE-PCRrep1_I1"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2023-12-05T19:07:15.624504+00:00",
"file_format": "fastq",
"file_size": 758913,
"href": "/sequence-files/IGVFFI9800CRJB/@@download/IGVFFI9800CRJB.fastq.gz",
"s3_uri": "s3://igvf-files/2023/12/05/b411a4e7-c183-4d99-8c3f-0604f065db50/IGVFFI9800CRJB.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_S3-BioRep1-FFRep2-BinE-PCRrep1_S12_I1_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI7455QOMR/",
"accession": "IGVFFI7455QOMR",
"aliases": [
"jesse-engreitz:220829_8merInsertion-Jurkat_NoStimulation-Amp_PPIF_promoter-BioRep1-FFrep2-BinE-PCRrep2_R1"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2023-12-05T18:47:48.570647+00:00",
"file_format": "fastq",
"file_size": 7789650,
"href": "/sequence-files/IGVFFI7455QOMR/@@download/IGVFFI7455QOMR.fastq.gz",
"s3_uri": "s3://igvf-files/2023/12/05/e4fd302c-671d-41a1-83a2-862eecf10dc5/IGVFFI7455QOMR.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_S3-BioRep1-FFRep2-BinE-PCRrep2_S68_R1_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI6164WJVT/",
"accession": "IGVFFI6164WJVT",
"aliases": [
"jesse-engreitz:220829_8merInsertion-Jurkat_NoStimulation-Amp_PPIF_promoter-BioRep1-FFrep2-BinE-PCRrep1_R2"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2023-12-05T18:54:11.105756+00:00",
"file_format": "fastq",
"file_size": 3147588,
"href": "/sequence-files/IGVFFI6164WJVT/@@download/IGVFFI6164WJVT.fastq.gz",
"s3_uri": "s3://igvf-files/2023/12/05/e9327b2c-4fed-42ed-a227-7c7122da437a/IGVFFI6164WJVT.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_S3-BioRep1-FFRep2-BinE-PCRrep1_S12_R2_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI9886JCGH/",
"accession": "IGVFFI9886JCGH",
"aliases": [
"jesse-engreitz:220829_8merInsertion-Jurkat_NoStimulation-Amp_PPIF_promoter-BioRep1-FFrep2-BinE-PCRrep2_I2"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2023-12-05T19:26:05.881349+00:00",
"file_format": "fastq",
"file_size": 3213746,
"href": "/sequence-files/IGVFFI9886JCGH/@@download/IGVFFI9886JCGH.fastq.gz",
"s3_uri": "s3://igvf-files/2023/12/05/e12c2915-e779-4773-a441-ab0a875392a0/IGVFFI9886JCGH.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_S3-BioRep1-FFRep2-BinE-PCRrep2_S68_I2_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI8365CSFD/",
"accession": "IGVFFI8365CSFD",
"aliases": [
"jesse-engreitz:220829_8merInsertion-Jurkat_NoStimulation-Amp_PPIF_promoter-BioRep1-FFrep2-BinE-PCRrep1_I2"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2023-12-05T19:19:44.885209+00:00",
"file_format": "fastq",
"file_size": 744844,
"href": "/sequence-files/IGVFFI8365CSFD/@@download/IGVFFI8365CSFD.fastq.gz",
"s3_uri": "s3://igvf-files/2023/12/05/97d6a8fc-105b-4220-b3ba-a6ed070eacc0/IGVFFI8365CSFD.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_S3-BioRep1-FFRep2-BinE-PCRrep1_S12_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": "2023-12-20T23:04:38.394120+00:00",
"samples": [
{
"@id": "/in-vitro-systems/IGVFSM0553VHCD/",
"@type": [
"InVitroSystem",
"Biosample",
"Sample",
"Item"
],
"accession": "IGVFSM0553VHCD",
"aliases": [
"jesse-engreitz:220829_8merInsertion-Jurkat_NoStimulation-Amp_PPIF_promoter-BioRep1-FFrep2-BinE"
],
"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 80-90% 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": "2023-12-05T18:41:30.149578+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": "ca06b183-752b-4f72-a44c-52c6d1aed75c"
}