{
"@context": "/terms/",
"@id": "/measurement-sets/IGVFDS1971XUME/",
"@type": [
"MeasurementSet",
"FileSet",
"Item"
],
"accession": "IGVFDS1971XUME",
"aliases": [
"jesse-engreitz:220829_8merInsertion-Jurkat_Stimulation-Amp_PPIF_promoter-BioRep3-FFrep1-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 [IGVFDS1971XUME](/measurement-sets/IGVFDS1971XUME/) has sequence file(s) [IGVFFI8307GOGG](/sequence-files/IGVFFI8307GOGG/), [IGVFFI5712LSRC](/sequence-files/IGVFFI5712LSRC/), [IGVFFI8778OIMO](/sequence-files/IGVFFI8778OIMO/), [IGVFFI3354NHCF](/sequence-files/IGVFFI3354NHCF/), [IGVFFI1626HXKH](/sequence-files/IGVFFI1626HXKH/), [IGVFFI7891VKWN](/sequence-files/IGVFFI7891VKWN/), [IGVFFI7683SBFU](/sequence-files/IGVFFI7683SBFU/), [IGVFFI6284IKHU](/sequence-files/IGVFFI6284IKHU/) 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/IGVFDS1971XUME/"
},
{
"category": "missing sequence specification",
"detail": "Measurement set [IGVFDS1971XUME](/measurement-sets/IGVFDS1971XUME/) has sequence file(s): [IGVFFI8307GOGG](/sequence-files/IGVFFI8307GOGG/), [IGVFFI5712LSRC](/sequence-files/IGVFFI5712LSRC/), [IGVFFI8778OIMO](/sequence-files/IGVFFI8778OIMO/), [IGVFFI3354NHCF](/sequence-files/IGVFFI3354NHCF/), [IGVFFI1626HXKH](/sequence-files/IGVFFI1626HXKH/), [IGVFFI7891VKWN](/sequence-files/IGVFFI7891VKWN/), [IGVFFI7683SBFU](/sequence-files/IGVFFI7683SBFU/), [IGVFFI6284IKHU](/sequence-files/IGVFFI6284IKHU/) 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/IGVFDS1971XUME/"
},
{
"category": "mismatched status",
"detail": "Released in vitro system [IGVFSM1037DJMF](/in-vitro-systems/IGVFSM1037DJMF/) 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/IGVFSM1037DJMF/"
}
],
"WARNING": [
{
"category": "missing auxiliary set",
"detail": "Measurement set [IGVFDS1971XUME](/measurement-sets/IGVFDS1971XUME/) 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/IGVFDS1971XUME/"
}
]
},
"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": "2023-11-30T22:48:23.651204+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/IGVFFI8307GOGG/",
"accession": "IGVFFI8307GOGG",
"aliases": [
"jesse-engreitz:220829_8merInsertion-Jurkat_Stimulation-Amp_PPIF_promoter-BioRep3-FFrep1-BinF-PCRrep2_R1"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2023-12-05T20:08:51.218124+00:00",
"file_format": "fastq",
"file_size": 7235654,
"href": "/sequence-files/IGVFFI8307GOGG/@@download/IGVFFI8307GOGG.fastq.gz",
"s3_uri": "s3://igvf-files/2023/12/05/f798b895-5fda-4d8c-8ff0-7e677859f823/IGVFFI8307GOGG.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-BinF-PCRrep2_S203_R1_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI5712LSRC/",
"accession": "IGVFFI5712LSRC",
"aliases": [
"jesse-engreitz:220829_8merInsertion-Jurkat_Stimulation-Amp_PPIF_promoter-BioRep3-FFrep1-BinF-PCRrep1_I2"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2023-12-05T20:00:37.876539+00:00",
"file_format": "fastq",
"file_size": 3027861,
"href": "/sequence-files/IGVFFI5712LSRC/@@download/IGVFFI5712LSRC.fastq.gz",
"s3_uri": "s3://igvf-files/2023/12/05/de6352f4-00b9-449b-aeb4-075f32b040bf/IGVFFI5712LSRC.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-BinF-PCRrep1_S146_I2_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI8778OIMO/",
"accession": "IGVFFI8778OIMO",
"aliases": [
"jesse-engreitz:220829_8merInsertion-Jurkat_Stimulation-Amp_PPIF_promoter-BioRep3-FFrep1-BinF-PCRrep1_I1"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2023-12-05T19:52:30.435012+00:00",
"file_format": "fastq",
"file_size": 3089544,
"href": "/sequence-files/IGVFFI8778OIMO/@@download/IGVFFI8778OIMO.fastq.gz",
"s3_uri": "s3://igvf-files/2023/12/05/58b6150d-b153-43c3-9b51-592dfaaf89ed/IGVFFI8778OIMO.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-BinF-PCRrep1_S146_I1_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI3354NHCF/",
"accession": "IGVFFI3354NHCF",
"aliases": [
"jesse-engreitz:220829_8merInsertion-Jurkat_Stimulation-Amp_PPIF_promoter-BioRep3-FFrep1-BinF-PCRrep1_R1"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2023-12-05T19:35:39.802087+00:00",
"file_format": "fastq",
"file_size": 7189180,
"href": "/sequence-files/IGVFFI3354NHCF/@@download/IGVFFI3354NHCF.fastq.gz",
"s3_uri": "s3://igvf-files/2023/12/05/27744615-ffc1-44ff-b7e4-97d74df31c9e/IGVFFI3354NHCF.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-BinF-PCRrep1_S146_R1_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI1626HXKH/",
"accession": "IGVFFI1626HXKH",
"aliases": [
"jesse-engreitz:220829_8merInsertion-Jurkat_Stimulation-Amp_PPIF_promoter-BioRep3-FFrep1-BinF-PCRrep2_I2"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2023-12-05T20:33:56.911821+00:00",
"file_format": "fastq",
"file_size": 3046162,
"href": "/sequence-files/IGVFFI1626HXKH/@@download/IGVFFI1626HXKH.fastq.gz",
"s3_uri": "s3://igvf-files/2023/12/05/56a10715-1362-4b3d-827f-0dfad90a63d4/IGVFFI1626HXKH.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-BinF-PCRrep2_S203_I2_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI7891VKWN/",
"accession": "IGVFFI7891VKWN",
"aliases": [
"jesse-engreitz:220829_8merInsertion-Jurkat_Stimulation-Amp_PPIF_promoter-BioRep3-FFrep1-BinF-PCRrep1_R2"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2023-12-05T19:44:06.932804+00:00",
"file_format": "fastq",
"file_size": 13482586,
"href": "/sequence-files/IGVFFI7891VKWN/@@download/IGVFFI7891VKWN.fastq.gz",
"s3_uri": "s3://igvf-files/2023/12/05/472ffc2e-4e35-4bc5-941b-02732fe54eb7/IGVFFI7891VKWN.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-BinF-PCRrep1_S146_R2_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI7683SBFU/",
"accession": "IGVFFI7683SBFU",
"aliases": [
"jesse-engreitz:220829_8merInsertion-Jurkat_Stimulation-Amp_PPIF_promoter-BioRep3-FFrep1-BinF-PCRrep2_I1"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2023-12-05T20:25:43.682686+00:00",
"file_format": "fastq",
"file_size": 3231929,
"href": "/sequence-files/IGVFFI7683SBFU/@@download/IGVFFI7683SBFU.fastq.gz",
"s3_uri": "s3://igvf-files/2023/12/05/80274e70-1928-409a-8c93-28bf71c36494/IGVFFI7683SBFU.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-BinF-PCRrep2_S203_I1_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI6284IKHU/",
"accession": "IGVFFI6284IKHU",
"aliases": [
"jesse-engreitz:220829_8merInsertion-Jurkat_Stimulation-Amp_PPIF_promoter-BioRep3-FFrep1-BinF-PCRrep2_R2"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2023-12-05T20:17:18.216209+00:00",
"file_format": "fastq",
"file_size": 13482504,
"href": "/sequence-files/IGVFFI6284IKHU/@@download/IGVFFI6284IKHU.fastq.gz",
"s3_uri": "s3://igvf-files/2023/12/05/2a291f2c-f164-42bd-a687-01718479269a/IGVFFI6284IKHU.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-BinF-PCRrep2_S203_R2_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": "2023-12-20T23:04:04.322219+00:00",
"samples": [
{
"@id": "/in-vitro-systems/IGVFSM1037DJMF/",
"@type": [
"InVitroSystem",
"Biosample",
"Sample",
"Item"
],
"accession": "IGVFSM1037DJMF",
"aliases": [
"jesse-engreitz:220829_8merInsertion-Jurkat_Stimulation-Amp_PPIF_promoter-BioRep3-FFrep1-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": "2023-12-05T19:35:39.802087+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": "70c7f38a-17ed-490b-94a0-d7a4b9597f6b"
}