{
"@context": "/terms/",
"@id": "/measurement-sets/IGVFDS4005DIAJ/",
"@type": [
"MeasurementSet",
"FileSet",
"Item"
],
"accession": "IGVFDS4005DIAJ",
"aliases": [
"jesse-engreitz:220829_8merInsertion-Jurkat_Stimulation-Amp_PPIF_promoter-BioRep3-FFrep1-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 [IGVFDS4005DIAJ](/measurement-sets/IGVFDS4005DIAJ/) has sequence file(s) [IGVFFI0944URFS](/sequence-files/IGVFFI0944URFS/), [IGVFFI2762TVLE](/sequence-files/IGVFFI2762TVLE/), [IGVFFI4268DZMI](/sequence-files/IGVFFI4268DZMI/), [IGVFFI7180YXVL](/sequence-files/IGVFFI7180YXVL/), [IGVFFI4693EBFS](/sequence-files/IGVFFI4693EBFS/), [IGVFFI7687ZVED](/sequence-files/IGVFFI7687ZVED/), [IGVFFI5153MQIX](/sequence-files/IGVFFI5153MQIX/), [IGVFFI9870OJQB](/sequence-files/IGVFFI9870OJQB/) 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/IGVFDS4005DIAJ/"
},
{
"category": "missing sequence specification",
"detail": "Measurement set [IGVFDS4005DIAJ](/measurement-sets/IGVFDS4005DIAJ/) has sequence file(s): [IGVFFI0944URFS](/sequence-files/IGVFFI0944URFS/), [IGVFFI2762TVLE](/sequence-files/IGVFFI2762TVLE/), [IGVFFI4268DZMI](/sequence-files/IGVFFI4268DZMI/), [IGVFFI7180YXVL](/sequence-files/IGVFFI7180YXVL/), [IGVFFI4693EBFS](/sequence-files/IGVFFI4693EBFS/), [IGVFFI7687ZVED](/sequence-files/IGVFFI7687ZVED/), [IGVFFI5153MQIX](/sequence-files/IGVFFI5153MQIX/), [IGVFFI9870OJQB](/sequence-files/IGVFFI9870OJQB/) 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/IGVFDS4005DIAJ/"
},
{
"category": "mismatched status",
"detail": "Released in vitro system [IGVFSM6920JBXJ](/in-vitro-systems/IGVFSM6920JBXJ/) 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/IGVFSM6920JBXJ/"
}
],
"WARNING": [
{
"category": "missing auxiliary set",
"detail": "Measurement set [IGVFDS4005DIAJ](/measurement-sets/IGVFDS4005DIAJ/) 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/IGVFDS4005DIAJ/"
}
]
},
"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": "2023-11-30T22:48:17.054822+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/IGVFFI0944URFS/",
"accession": "IGVFFI0944URFS",
"aliases": [
"jesse-engreitz:220829_8merInsertion-Jurkat_Stimulation-Amp_PPIF_promoter-BioRep3-FFrep1-BinA-PCRrep2_I2"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2023-12-05T20:33:12.683542+00:00",
"file_format": "fastq",
"file_size": 3218226,
"href": "/sequence-files/IGVFFI0944URFS/@@download/IGVFFI0944URFS.fastq.gz",
"s3_uri": "s3://igvf-files/2023/12/05/deee2f1d-1199-43b4-884f-de98c03c5978/IGVFFI0944URFS.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_S17-BioRep3-FFRep1-BinA-PCRrep2_S198_I2_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI2762TVLE/",
"accession": "IGVFFI2762TVLE",
"aliases": [
"jesse-engreitz:220829_8merInsertion-Jurkat_Stimulation-Amp_PPIF_promoter-BioRep3-FFrep1-BinA-PCRrep1_R1"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2023-12-05T19:34:55.911581+00:00",
"file_format": "fastq",
"file_size": 7555164,
"href": "/sequence-files/IGVFFI2762TVLE/@@download/IGVFFI2762TVLE.fastq.gz",
"s3_uri": "s3://igvf-files/2023/12/05/4f2c4156-aef6-4d5f-9728-f792f5f22b75/IGVFFI2762TVLE.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_S17-BioRep3-FFRep1-BinA-PCRrep1_S141_R1_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI4268DZMI/",
"accession": "IGVFFI4268DZMI",
"aliases": [
"jesse-engreitz:220829_8merInsertion-Jurkat_Stimulation-Amp_PPIF_promoter-BioRep3-FFrep1-BinA-PCRrep1_I2"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2023-12-05T19:59:54.225910+00:00",
"file_format": "fastq",
"file_size": 3141035,
"href": "/sequence-files/IGVFFI4268DZMI/@@download/IGVFFI4268DZMI.fastq.gz",
"s3_uri": "s3://igvf-files/2023/12/05/6da184f4-6c99-4f4d-8200-f56f166e27f7/IGVFFI4268DZMI.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_S17-BioRep3-FFRep1-BinA-PCRrep1_S141_I2_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI7180YXVL/",
"accession": "IGVFFI7180YXVL",
"aliases": [
"jesse-engreitz:220829_8merInsertion-Jurkat_Stimulation-Amp_PPIF_promoter-BioRep3-FFrep1-BinA-PCRrep2_R2"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2023-12-05T20:16:32.474189+00:00",
"file_format": "fastq",
"file_size": 14062307,
"href": "/sequence-files/IGVFFI7180YXVL/@@download/IGVFFI7180YXVL.fastq.gz",
"s3_uri": "s3://igvf-files/2023/12/05/c06fd4f1-4497-4998-9f37-0afdef5d5f8b/IGVFFI7180YXVL.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_S17-BioRep3-FFRep1-BinA-PCRrep2_S198_R2_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI4693EBFS/",
"accession": "IGVFFI4693EBFS",
"aliases": [
"jesse-engreitz:220829_8merInsertion-Jurkat_Stimulation-Amp_PPIF_promoter-BioRep3-FFrep1-BinA-PCRrep1_R2"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2023-12-05T19:43:20.766178+00:00",
"file_format": "fastq",
"file_size": 13728809,
"href": "/sequence-files/IGVFFI4693EBFS/@@download/IGVFFI4693EBFS.fastq.gz",
"s3_uri": "s3://igvf-files/2023/12/05/c3f36187-3a85-4450-86b1-de135df48869/IGVFFI4693EBFS.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_S17-BioRep3-FFRep1-BinA-PCRrep1_S141_R2_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI7687ZVED/",
"accession": "IGVFFI7687ZVED",
"aliases": [
"jesse-engreitz:220829_8merInsertion-Jurkat_Stimulation-Amp_PPIF_promoter-BioRep3-FFrep1-BinA-PCRrep2_R1"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2023-12-05T20:08:07.219383+00:00",
"file_format": "fastq",
"file_size": 7718929,
"href": "/sequence-files/IGVFFI7687ZVED/@@download/IGVFFI7687ZVED.fastq.gz",
"s3_uri": "s3://igvf-files/2023/12/05/1f3c64e6-f881-41e2-a87c-455c48d047cf/IGVFFI7687ZVED.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_S17-BioRep3-FFRep1-BinA-PCRrep2_S198_R1_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI5153MQIX/",
"accession": "IGVFFI5153MQIX",
"aliases": [
"jesse-engreitz:220829_8merInsertion-Jurkat_Stimulation-Amp_PPIF_promoter-BioRep3-FFrep1-BinA-PCRrep1_I1"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2023-12-05T19:51:47.158192+00:00",
"file_format": "fastq",
"file_size": 3298231,
"href": "/sequence-files/IGVFFI5153MQIX/@@download/IGVFFI5153MQIX.fastq.gz",
"s3_uri": "s3://igvf-files/2023/12/05/ab1b766d-d18b-4736-a414-c524513e7acf/IGVFFI5153MQIX.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_S17-BioRep3-FFRep1-BinA-PCRrep1_S141_I1_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI9870OJQB/",
"accession": "IGVFFI9870OJQB",
"aliases": [
"jesse-engreitz:220829_8merInsertion-Jurkat_Stimulation-Amp_PPIF_promoter-BioRep3-FFrep1-BinA-PCRrep2_I1"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2023-12-05T20:25:00.478308+00:00",
"file_format": "fastq",
"file_size": 3256373,
"href": "/sequence-files/IGVFFI9870OJQB/@@download/IGVFFI9870OJQB.fastq.gz",
"s3_uri": "s3://igvf-files/2023/12/05/43d765b3-396c-4080-87b5-f0bed0b1d51c/IGVFFI9870OJQB.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_S17-BioRep3-FFRep1-BinA-PCRrep2_S198_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": "2023-12-20T23:04:08.301147+00:00",
"samples": [
{
"@id": "/in-vitro-systems/IGVFSM6920JBXJ/",
"@type": [
"InVitroSystem",
"Biosample",
"Sample",
"Item"
],
"accession": "IGVFSM6920JBXJ",
"aliases": [
"jesse-engreitz:220829_8merInsertion-Jurkat_Stimulation-Amp_PPIF_promoter-BioRep3-FFrep1-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) 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": "2023-12-05T19:34:55.911581+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": "c380fbb6-d209-476b-aa9f-10e39e07e0a3"
}