{
"@context": "/terms/",
"@id": "/measurement-sets/IGVFDS4306VGPH/",
"@type": [
"MeasurementSet",
"FileSet",
"Item"
],
"accession": "IGVFDS4306VGPH",
"aliases": [
"jesse-engreitz:220829_8merInsertion-Jurkat_Stimulation-Amp_PPIF_promoter-BioRep1-FFrep1-FACS_Input_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 [IGVFSM9972NTOV](/in-vitro-systems/IGVFSM9972NTOV/) 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/IGVFSM9972NTOV/"
},
{
"category": "missing sequencing kit",
"detail": "Measurement set [IGVFDS4306VGPH](/measurement-sets/IGVFDS4306VGPH/) has sequence file(s) [IGVFFI3115ENZO](/sequence-files/IGVFFI3115ENZO/), [IGVFFI9082CVDX](/sequence-files/IGVFFI9082CVDX/), [IGVFFI8616FHAG](/sequence-files/IGVFFI8616FHAG/), [IGVFFI6878TXOZ](/sequence-files/IGVFFI6878TXOZ/), [IGVFFI2334IBSN](/sequence-files/IGVFFI2334IBSN/), [IGVFFI1347NRZV](/sequence-files/IGVFFI1347NRZV/), [IGVFFI0503LALK](/sequence-files/IGVFFI0503LALK/), [IGVFFI5387WIYE](/sequence-files/IGVFFI5387WIYE/) 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/IGVFDS4306VGPH/"
},
{
"category": "missing sequence specification",
"detail": "Measurement set [IGVFDS4306VGPH](/measurement-sets/IGVFDS4306VGPH/) has sequence file(s): [IGVFFI3115ENZO](/sequence-files/IGVFFI3115ENZO/), [IGVFFI9082CVDX](/sequence-files/IGVFFI9082CVDX/), [IGVFFI8616FHAG](/sequence-files/IGVFFI8616FHAG/), [IGVFFI6878TXOZ](/sequence-files/IGVFFI6878TXOZ/), [IGVFFI2334IBSN](/sequence-files/IGVFFI2334IBSN/), [IGVFFI1347NRZV](/sequence-files/IGVFFI1347NRZV/), [IGVFFI0503LALK](/sequence-files/IGVFFI0503LALK/), [IGVFFI5387WIYE](/sequence-files/IGVFFI5387WIYE/) 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/IGVFDS4306VGPH/"
}
],
"WARNING": [
{
"category": "missing auxiliary set",
"detail": "Measurement set [IGVFDS4306VGPH](/measurement-sets/IGVFDS4306VGPH/) 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/IGVFDS4306VGPH/"
},
{
"category": "missing targeted genes",
"detail": "Measurement set [IGVFDS4306VGPH](/measurement-sets/IGVFDS4306VGPH/) has no `targeted_genes`. ChIP-seq and CRISPR flow cytometry assays are expected to specify targeted gene(s).",
"level": 40,
"level_name": "WARNING",
"name": "audit_targeted_genes",
"path": "/measurement-sets/IGVFDS4306VGPH/"
}
]
},
"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": [],
"control_type": "unsorted FACS input",
"creation_timestamp": "2023-11-30T22:47:46.271796+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/IGVFFI3115ENZO/",
"accession": "IGVFFI3115ENZO",
"aliases": [
"jesse-engreitz:220829_8merInsertion-Jurkat_Stimulation-Amp_PPIF_promoter-BioRep1-FFrep1-FACS_Input-PCRrep2_R2"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2023-12-05T20:13:10.202418+00:00",
"file_format": "fastq",
"file_size": 13898835,
"href": "/sequence-files/IGVFFI3115ENZO/@@download/IGVFFI3115ENZO.fastq.gz",
"s3_uri": "s3://igvf-files/2023/12/05/029afb2e-65d7-434a-a5cf-e34df78f6258/IGVFFI3115ENZO.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_S12-BioRep1-FFRep1-BinAll-PCRrep2_S176_R2_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI9082CVDX/",
"accession": "IGVFFI9082CVDX",
"aliases": [
"jesse-engreitz:220829_8merInsertion-Jurkat_Stimulation-Amp_PPIF_promoter-BioRep1-FFrep1-FACS_Input-PCRrep1_I1"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2023-12-05T19:48:33.359989+00:00",
"file_format": "fastq",
"file_size": 3388656,
"href": "/sequence-files/IGVFFI9082CVDX/@@download/IGVFFI9082CVDX.fastq.gz",
"s3_uri": "s3://igvf-files/2023/12/05/522e9dc1-1cd6-4253-af22-da35bce6bb60/IGVFFI9082CVDX.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_S12-BioRep1-FFRep1-BinAll-PCRrep1_S119_I1_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI8616FHAG/",
"accession": "IGVFFI8616FHAG",
"aliases": [
"jesse-engreitz:220829_8merInsertion-Jurkat_Stimulation-Amp_PPIF_promoter-BioRep1-FFrep1-FACS_Input-PCRrep2_I2"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2023-12-05T20:30:00.510959+00:00",
"file_format": "fastq",
"file_size": 3137857,
"href": "/sequence-files/IGVFFI8616FHAG/@@download/IGVFFI8616FHAG.fastq.gz",
"s3_uri": "s3://igvf-files/2023/12/05/c45caefb-62d6-4b7f-af04-f6b3062b7f71/IGVFFI8616FHAG.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_S12-BioRep1-FFRep1-BinAll-PCRrep2_S176_I2_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI6878TXOZ/",
"accession": "IGVFFI6878TXOZ",
"aliases": [
"jesse-engreitz:220829_8merInsertion-Jurkat_Stimulation-Amp_PPIF_promoter-BioRep1-FFrep1-FACS_Input-PCRrep1_I2"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2023-12-05T19:56:42.854544+00:00",
"file_format": "fastq",
"file_size": 3259192,
"href": "/sequence-files/IGVFFI6878TXOZ/@@download/IGVFFI6878TXOZ.fastq.gz",
"s3_uri": "s3://igvf-files/2023/12/05/7e805eec-1c10-4219-8855-32e184038ec5/IGVFFI6878TXOZ.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_S12-BioRep1-FFRep1-BinAll-PCRrep1_S119_I2_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI2334IBSN/",
"accession": "IGVFFI2334IBSN",
"aliases": [
"jesse-engreitz:220829_8merInsertion-Jurkat_Stimulation-Amp_PPIF_promoter-BioRep1-FFrep1-FACS_Input-PCRrep2_R1"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2023-12-05T20:04:51.240032+00:00",
"file_format": "fastq",
"file_size": 7514075,
"href": "/sequence-files/IGVFFI2334IBSN/@@download/IGVFFI2334IBSN.fastq.gz",
"s3_uri": "s3://igvf-files/2023/12/05/2c8a48f2-7af2-4a1a-973f-746136ea3c84/IGVFFI2334IBSN.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_S12-BioRep1-FFRep1-BinAll-PCRrep2_S176_R1_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI1347NRZV/",
"accession": "IGVFFI1347NRZV",
"aliases": [
"jesse-engreitz:220829_8merInsertion-Jurkat_Stimulation-Amp_PPIF_promoter-BioRep1-FFrep1-FACS_Input-PCRrep1_R2"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2023-12-05T19:39:58.954122+00:00",
"file_format": "fastq",
"file_size": 14439446,
"href": "/sequence-files/IGVFFI1347NRZV/@@download/IGVFFI1347NRZV.fastq.gz",
"s3_uri": "s3://igvf-files/2023/12/05/a96f75e8-b63d-40e0-8535-aa30268ca1f9/IGVFFI1347NRZV.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_S12-BioRep1-FFRep1-BinAll-PCRrep1_S119_R2_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI0503LALK/",
"accession": "IGVFFI0503LALK",
"aliases": [
"jesse-engreitz:220829_8merInsertion-Jurkat_Stimulation-Amp_PPIF_promoter-BioRep1-FFrep1-FACS_Input-PCRrep2_I1"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2023-12-05T20:21:40.247991+00:00",
"file_format": "fastq",
"file_size": 3151551,
"href": "/sequence-files/IGVFFI0503LALK/@@download/IGVFFI0503LALK.fastq.gz",
"s3_uri": "s3://igvf-files/2023/12/05/1e4b1220-207e-4246-ae44-4b76ba5e6082/IGVFFI0503LALK.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_S12-BioRep1-FFRep1-BinAll-PCRrep2_S176_I1_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI5387WIYE/",
"accession": "IGVFFI5387WIYE",
"aliases": [
"jesse-engreitz:220829_8merInsertion-Jurkat_Stimulation-Amp_PPIF_promoter-BioRep1-FFrep1-FACS_Input-PCRrep1_R1"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2023-12-05T19:31:37.498182+00:00",
"file_format": "fastq",
"file_size": 7849057,
"href": "/sequence-files/IGVFFI5387WIYE/@@download/IGVFFI5387WIYE.fastq.gz",
"s3_uri": "s3://igvf-files/2023/12/05/956da694-9ff5-42d2-8188-45fc8072bccc/IGVFFI5387WIYE.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_S12-BioRep1-FFRep1-BinAll-PCRrep1_S119_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": "2023-12-20T23:03:41.841193+00:00",
"samples": [
{
"@id": "/in-vitro-systems/IGVFSM9972NTOV/",
"@type": [
"InVitroSystem",
"Biosample",
"Sample",
"Item"
],
"accession": "IGVFSM9972NTOV",
"aliases": [
"jesse-engreitz:220829_8merInsertion-Jurkat_Stimulation-Amp_PPIF_promoter-BioRep1-FFrep1-FACS_Input"
],
"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 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": "2023-12-05T19:31:37.498182+00:00",
"summary": "unsorted FACS input CRISPR prime editing Variant-EFFECTS integrating a guide (sgRNA) library targeting sequence variants in a genomic locus",
"uuid": "b3cc3799-f93c-4795-bfb4-5c23a9674af9"
}