{
"@context": "/terms/",
"@id": "/measurement-sets/IGVFDS9738RCWL/",
"@type": [
"MeasurementSet",
"FileSet",
"Item"
],
"accession": "IGVFDS9738RCWL",
"aliases": [
"jesse-engreitz:220829_8merInsertion-Jurkat_Stimulation-Amp_PPIF_promoter-BioRep3-FFrep2-BinF_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 [IGVFDS9738RCWL](/measurement-sets/IGVFDS9738RCWL/) has sequence file(s) [IGVFFI0095FGAT](/sequence-files/IGVFFI0095FGAT/), [IGVFFI7538ERWB](/sequence-files/IGVFFI7538ERWB/), [IGVFFI0181XKEH](/sequence-files/IGVFFI0181XKEH/), [IGVFFI4871VTJE](/sequence-files/IGVFFI4871VTJE/), [IGVFFI9433DMQK](/sequence-files/IGVFFI9433DMQK/), [IGVFFI5065RJEY](/sequence-files/IGVFFI5065RJEY/), [IGVFFI3349HGTD](/sequence-files/IGVFFI3349HGTD/), [IGVFFI6539PSRS](/sequence-files/IGVFFI6539PSRS/) 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/IGVFDS9738RCWL/"
},
{
"category": "missing sequence specification",
"detail": "Measurement set [IGVFDS9738RCWL](/measurement-sets/IGVFDS9738RCWL/) has sequence file(s): [IGVFFI0095FGAT](/sequence-files/IGVFFI0095FGAT/), [IGVFFI7538ERWB](/sequence-files/IGVFFI7538ERWB/), [IGVFFI0181XKEH](/sequence-files/IGVFFI0181XKEH/), [IGVFFI4871VTJE](/sequence-files/IGVFFI4871VTJE/), [IGVFFI9433DMQK](/sequence-files/IGVFFI9433DMQK/), [IGVFFI5065RJEY](/sequence-files/IGVFFI5065RJEY/), [IGVFFI3349HGTD](/sequence-files/IGVFFI3349HGTD/), [IGVFFI6539PSRS](/sequence-files/IGVFFI6539PSRS/) 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/IGVFDS9738RCWL/"
},
{
"category": "mismatched status",
"detail": "Released in vitro system [IGVFSM8638GWPD](/in-vitro-systems/IGVFSM8638GWPD/) 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/IGVFSM8638GWPD/"
}
],
"WARNING": [
{
"category": "missing auxiliary set",
"detail": "Measurement set [IGVFDS9738RCWL](/measurement-sets/IGVFDS9738RCWL/) 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/IGVFDS9738RCWL/"
}
]
},
"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": "2023-11-30T22:48:31.647124+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/IGVFFI0095FGAT/",
"accession": "IGVFFI0095FGAT",
"aliases": [
"jesse-engreitz:220829_8merInsertion-Jurkat_Stimulation-Amp_PPIF_promoter-BioRep3-FFrep2-BinF-PCRrep1_I2"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2023-12-05T20:01:38.722431+00:00",
"file_format": "fastq",
"file_size": 3140981,
"href": "/sequence-files/IGVFFI0095FGAT/@@download/IGVFFI0095FGAT.fastq.gz",
"s3_uri": "s3://igvf-files/2023/12/05/683c4bbf-1aa5-4506-a2a5-fabb2c7267f9/IGVFFI0095FGAT.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_S18-BioRep3-FFRep2-BinF-PCRrep1_S153_I2_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI7538ERWB/",
"accession": "IGVFFI7538ERWB",
"aliases": [
"jesse-engreitz:220829_8merInsertion-Jurkat_Stimulation-Amp_PPIF_promoter-BioRep3-FFrep2-BinF-PCRrep1_R2"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2023-12-05T19:45:10.864914+00:00",
"file_format": "fastq",
"file_size": 14017267,
"href": "/sequence-files/IGVFFI7538ERWB/@@download/IGVFFI7538ERWB.fastq.gz",
"s3_uri": "s3://igvf-files/2023/12/05/96830ef8-bca3-44b7-babf-c8aafbfd2587/IGVFFI7538ERWB.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_S18-BioRep3-FFRep2-BinF-PCRrep1_S153_R2_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI0181XKEH/",
"accession": "IGVFFI0181XKEH",
"aliases": [
"jesse-engreitz:220829_8merInsertion-Jurkat_Stimulation-Amp_PPIF_promoter-BioRep3-FFrep2-BinF-PCRrep1_R1"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2023-12-05T19:36:42.241388+00:00",
"file_format": "fastq",
"file_size": 7467872,
"href": "/sequence-files/IGVFFI0181XKEH/@@download/IGVFFI0181XKEH.fastq.gz",
"s3_uri": "s3://igvf-files/2023/12/05/3f84805f-7481-4a72-b57c-3a418e08c1a2/IGVFFI0181XKEH.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_S18-BioRep3-FFRep2-BinF-PCRrep1_S153_R1_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI4871VTJE/",
"accession": "IGVFFI4871VTJE",
"aliases": [
"jesse-engreitz:220829_8merInsertion-Jurkat_Stimulation-Amp_PPIF_promoter-BioRep3-FFrep2-BinF-PCRrep1_I1"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2023-12-05T19:53:31.376714+00:00",
"file_format": "fastq",
"file_size": 3183015,
"href": "/sequence-files/IGVFFI4871VTJE/@@download/IGVFFI4871VTJE.fastq.gz",
"s3_uri": "s3://igvf-files/2023/12/05/a78b2da2-0089-4a3d-a119-5cb9e0ccbc73/IGVFFI4871VTJE.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_S18-BioRep3-FFRep2-BinF-PCRrep1_S153_I1_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI9433DMQK/",
"accession": "IGVFFI9433DMQK",
"aliases": [
"jesse-engreitz:220829_8merInsertion-Jurkat_Stimulation-Amp_PPIF_promoter-BioRep3-FFrep2-BinF-PCRrep2_I2"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2023-12-05T20:34:57.941136+00:00",
"file_format": "fastq",
"file_size": 3196762,
"href": "/sequence-files/IGVFFI9433DMQK/@@download/IGVFFI9433DMQK.fastq.gz",
"s3_uri": "s3://igvf-files/2023/12/05/46c66a25-a32c-4db9-aa9b-97406ba2ef01/IGVFFI9433DMQK.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_S18-BioRep3-FFRep2-BinF-PCRrep2_S210_I2_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI5065RJEY/",
"accession": "IGVFFI5065RJEY",
"aliases": [
"jesse-engreitz:220829_8merInsertion-Jurkat_Stimulation-Amp_PPIF_promoter-BioRep3-FFrep2-BinF-PCRrep2_R1"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2023-12-05T20:09:53.461685+00:00",
"file_format": "fastq",
"file_size": 7653641,
"href": "/sequence-files/IGVFFI5065RJEY/@@download/IGVFFI5065RJEY.fastq.gz",
"s3_uri": "s3://igvf-files/2023/12/05/73509c47-d78c-4594-904a-e139229791d8/IGVFFI5065RJEY.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_S18-BioRep3-FFRep2-BinF-PCRrep2_S210_R1_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI3349HGTD/",
"accession": "IGVFFI3349HGTD",
"aliases": [
"jesse-engreitz:220829_8merInsertion-Jurkat_Stimulation-Amp_PPIF_promoter-BioRep3-FFrep2-BinF-PCRrep2_R2"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2023-12-05T20:18:21.951174+00:00",
"file_format": "fastq",
"file_size": 14243421,
"href": "/sequence-files/IGVFFI3349HGTD/@@download/IGVFFI3349HGTD.fastq.gz",
"s3_uri": "s3://igvf-files/2023/12/05/962927af-d6c3-44a8-b453-684ebad8a37d/IGVFFI3349HGTD.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_S18-BioRep3-FFRep2-BinF-PCRrep2_S210_R2_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI6539PSRS/",
"accession": "IGVFFI6539PSRS",
"aliases": [
"jesse-engreitz:220829_8merInsertion-Jurkat_Stimulation-Amp_PPIF_promoter-BioRep3-FFrep2-BinF-PCRrep2_I1"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2023-12-05T20:26:44.853230+00:00",
"file_format": "fastq",
"file_size": 3293948,
"href": "/sequence-files/IGVFFI6539PSRS/@@download/IGVFFI6539PSRS.fastq.gz",
"s3_uri": "s3://igvf-files/2023/12/05/79a309a4-dbe5-46ec-8bf5-a8de6bae5be2/IGVFFI6539PSRS.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_S18-BioRep3-FFRep2-BinF-PCRrep2_S210_I1_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": "2023-12-20T23:03:53.832591+00:00",
"samples": [
{
"@id": "/in-vitro-systems/IGVFSM8638GWPD/",
"@type": [
"InVitroSystem",
"Biosample",
"Sample",
"Item"
],
"accession": "IGVFSM8638GWPD",
"aliases": [
"jesse-engreitz:220829_8merInsertion-Jurkat_Stimulation-Amp_PPIF_promoter-BioRep3-FFrep2-BinF"
],
"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 90-100% 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), transfected with a guide library",
"taxa": "Homo sapiens",
"treatments": [
{
"@id": "/treatments/df02c0d4-f796-4f77-bfbc-388cdbfcc615/",
"status": "released",
"treatment_term_name": "T-cell surface glycoprotein CD3 gamma chain"
},
{
"@id": "/treatments/42b3c61d-38de-4bd2-bb39-33c125a417cb/",
"status": "released",
"treatment_term_name": "phorbol 13-acetate 12-myristate"
}
]
}
],
"schema_version": "23",
"status": "released",
"submitted_by": {
"@id": "/users/f9e7cd82-a407-4a20-89ee-f4dc668b0cbe/",
"title": "Michael Montgomery"
},
"submitted_files_timestamp": "2023-12-05T19:36:42.241388+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": "fb30f5f3-a7fc-435a-8ec3-890a56d9703f"
}