{
"@context": "/terms/",
"@id": "/measurement-sets/IGVFDS7638KDSZ/",
"@type": [
"MeasurementSet",
"FileSet",
"Item"
],
"accession": "IGVFDS7638KDSZ",
"aliases": [
"jesse-engreitz:220829_8merInsertion-Jurkat_Stimulation-Amp_PPIF_promoter-BioRep4-FFrep2-BinC_AmpliconSequencing"
],
"assay_term": {
"@id": "/assay-terms/OBI_0003661/",
"status": "released",
"term_name": "in vitro CRISPR screen using flow cytometry"
},
"audit": {
"INTERNAL_ACTION": [
{
"category": "mismatched status",
"detail": "Released in vitro system [IGVFSM8232SHRI](/in-vitro-systems/IGVFSM8232SHRI/) 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/IGVFSM8232SHRI/"
},
{
"category": "missing sequencing kit",
"detail": "Measurement set [IGVFDS7638KDSZ](/measurement-sets/IGVFDS7638KDSZ/) has sequence file(s) [IGVFFI3133PEYI](/sequence-files/IGVFFI3133PEYI/), [IGVFFI8001JJVA](/sequence-files/IGVFFI8001JJVA/), [IGVFFI3130LNKC](/sequence-files/IGVFFI3130LNKC/), [IGVFFI2777CCKX](/sequence-files/IGVFFI2777CCKX/), [IGVFFI9804QQWL](/sequence-files/IGVFFI9804QQWL/), [IGVFFI8350EPHO](/sequence-files/IGVFFI8350EPHO/), [IGVFFI4977TSES](/sequence-files/IGVFFI4977TSES/), [IGVFFI8369ZSHJ](/sequence-files/IGVFFI8369ZSHJ/) 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/IGVFDS7638KDSZ/"
},
{
"category": "missing sequence specification",
"detail": "Measurement set [IGVFDS7638KDSZ](/measurement-sets/IGVFDS7638KDSZ/) has sequence file(s): [IGVFFI3133PEYI](/sequence-files/IGVFFI3133PEYI/), [IGVFFI8001JJVA](/sequence-files/IGVFFI8001JJVA/), [IGVFFI3130LNKC](/sequence-files/IGVFFI3130LNKC/), [IGVFFI2777CCKX](/sequence-files/IGVFFI2777CCKX/), [IGVFFI9804QQWL](/sequence-files/IGVFFI9804QQWL/), [IGVFFI8350EPHO](/sequence-files/IGVFFI8350EPHO/), [IGVFFI4977TSES](/sequence-files/IGVFFI4977TSES/), [IGVFFI8369ZSHJ](/sequence-files/IGVFFI8369ZSHJ/) 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/IGVFDS7638KDSZ/"
}
],
"WARNING": [
{
"category": "missing auxiliary set",
"detail": "Measurement set [IGVFDS7638KDSZ](/measurement-sets/IGVFDS7638KDSZ/) 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/IGVFDS7638KDSZ/"
}
]
},
"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": "2023-11-30T22:48:43.474067+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/IGVFFI3133PEYI/",
"accession": "IGVFFI3133PEYI",
"aliases": [
"jesse-engreitz:220829_8merInsertion-Jurkat_Stimulation-Amp_PPIF_promoter-BioRep4-FFrep2-BinC-PCRrep1_I2"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2023-12-05T20:03:14.505935+00:00",
"file_format": "fastq",
"file_size": 3282212,
"href": "/sequence-files/IGVFFI3133PEYI/@@download/IGVFFI3133PEYI.fastq.gz",
"s3_uri": "s3://igvf-files/2023/12/05/16e4e294-ab53-4dea-8c93-7feaba1e3936/IGVFFI3133PEYI.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_S20-BioRep4-FFRep2-BinC-PCRrep1_S164_I2_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI8001JJVA/",
"accession": "IGVFFI8001JJVA",
"aliases": [
"jesse-engreitz:220829_8merInsertion-Jurkat_Stimulation-Amp_PPIF_promoter-BioRep4-FFrep2-BinC-PCRrep2_R2"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2023-12-05T20:20:02.438855+00:00",
"file_format": "fastq",
"file_size": 14478740,
"href": "/sequence-files/IGVFFI8001JJVA/@@download/IGVFFI8001JJVA.fastq.gz",
"s3_uri": "s3://igvf-files/2023/12/05/75d48b70-e78b-4929-886d-ff6622a3185b/IGVFFI8001JJVA.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_S20-BioRep4-FFRep2-BinC-PCRrep2_S221_R2_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI3130LNKC/",
"accession": "IGVFFI3130LNKC",
"aliases": [
"jesse-engreitz:220829_8merInsertion-Jurkat_Stimulation-Amp_PPIF_promoter-BioRep4-FFrep2-BinC-PCRrep1_R2"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2023-12-05T19:46:51.079633+00:00",
"file_format": "fastq",
"file_size": 14516743,
"href": "/sequence-files/IGVFFI3130LNKC/@@download/IGVFFI3130LNKC.fastq.gz",
"s3_uri": "s3://igvf-files/2023/12/05/c34ab6eb-f166-483a-ba3e-caef0d73bc05/IGVFFI3130LNKC.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_S20-BioRep4-FFRep2-BinC-PCRrep1_S164_R2_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI2777CCKX/",
"accession": "IGVFFI2777CCKX",
"aliases": [
"jesse-engreitz:220829_8merInsertion-Jurkat_Stimulation-Amp_PPIF_promoter-BioRep4-FFrep2-BinC-PCRrep1_I1"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2023-12-05T19:55:07.398325+00:00",
"file_format": "fastq",
"file_size": 3396766,
"href": "/sequence-files/IGVFFI2777CCKX/@@download/IGVFFI2777CCKX.fastq.gz",
"s3_uri": "s3://igvf-files/2023/12/05/fa9ad73b-e0e6-482b-b25a-511142adb4fe/IGVFFI2777CCKX.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_S20-BioRep4-FFRep2-BinC-PCRrep1_S164_I1_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI9804QQWL/",
"accession": "IGVFFI9804QQWL",
"aliases": [
"jesse-engreitz:220829_8merInsertion-Jurkat_Stimulation-Amp_PPIF_promoter-BioRep4-FFrep2-BinC-PCRrep2_I1"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2023-12-05T20:28:21.015814+00:00",
"file_format": "fastq",
"file_size": 3488475,
"href": "/sequence-files/IGVFFI9804QQWL/@@download/IGVFFI9804QQWL.fastq.gz",
"s3_uri": "s3://igvf-files/2023/12/05/0dd4ef51-47fd-4a32-9ccc-4bd4d0603ff0/IGVFFI9804QQWL.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_S20-BioRep4-FFRep2-BinC-PCRrep2_S221_I1_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI8350EPHO/",
"accession": "IGVFFI8350EPHO",
"aliases": [
"jesse-engreitz:220829_8merInsertion-Jurkat_Stimulation-Amp_PPIF_promoter-BioRep4-FFrep2-BinC-PCRrep1_R1"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2023-12-05T19:38:19.324465+00:00",
"file_format": "fastq",
"file_size": 7890780,
"href": "/sequence-files/IGVFFI8350EPHO/@@download/IGVFFI8350EPHO.fastq.gz",
"s3_uri": "s3://igvf-files/2023/12/05/52aea34b-48a9-4076-ab24-31c86c390bb5/IGVFFI8350EPHO.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_S20-BioRep4-FFRep2-BinC-PCRrep1_S164_R1_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI4977TSES/",
"accession": "IGVFFI4977TSES",
"aliases": [
"jesse-engreitz:220829_8merInsertion-Jurkat_Stimulation-Amp_PPIF_promoter-BioRep4-FFrep2-BinC-PCRrep2_I2"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2023-12-05T20:36:33.960816+00:00",
"file_format": "fastq",
"file_size": 3277498,
"href": "/sequence-files/IGVFFI4977TSES/@@download/IGVFFI4977TSES.fastq.gz",
"s3_uri": "s3://igvf-files/2023/12/05/5f35259b-8006-49a2-a8bd-f305ac5de3da/IGVFFI4977TSES.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_S20-BioRep4-FFRep2-BinC-PCRrep2_S221_I2_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI8369ZSHJ/",
"accession": "IGVFFI8369ZSHJ",
"aliases": [
"jesse-engreitz:220829_8merInsertion-Jurkat_Stimulation-Amp_PPIF_promoter-BioRep4-FFrep2-BinC-PCRrep2_R1"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2023-12-05T20:11:30.905374+00:00",
"file_format": "fastq",
"file_size": 7834800,
"href": "/sequence-files/IGVFFI8369ZSHJ/@@download/IGVFFI8369ZSHJ.fastq.gz",
"s3_uri": "s3://igvf-files/2023/12/05/bee5eaa9-9aeb-44f0-a4b4-a437f086cef8/IGVFFI8369ZSHJ.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_S20-BioRep4-FFRep2-BinC-PCRrep2_S221_R1_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": "2023-12-20T23:03:47.404170+00:00",
"samples": [
{
"@id": "/in-vitro-systems/IGVFSM8232SHRI/",
"@type": [
"InVitroSystem",
"Biosample",
"Sample",
"Item"
],
"accession": "IGVFSM8232SHRI",
"aliases": [
"jesse-engreitz:220829_8merInsertion-Jurkat_Stimulation-Amp_PPIF_promoter-BioRep4-FFrep2-BinC"
],
"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 35-45% 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": "2023-12-05T19:38:19.324465+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": "8a10d3a4-1c31-4d77-a790-54a878a56496"
}