{
"@context": "/terms/",
"@id": "/measurement-sets/IGVFDS1370QEJF/",
"@type": [
"MeasurementSet",
"FileSet",
"Item"
],
"accession": "IGVFDS1370QEJF",
"aliases": [
"jesse-engreitz:220829_8merInsertion-Jurkat_Stimulation-Amp_PPIF_promoter-BioRep1-FFrep2-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": "missing sequencing kit",
"detail": "Measurement set [IGVFDS1370QEJF](/measurement-sets/IGVFDS1370QEJF/) has sequence file(s) [IGVFFI3324IWGH](/sequence-files/IGVFFI3324IWGH/), [IGVFFI6156DULO](/sequence-files/IGVFFI6156DULO/), [IGVFFI7213YRKN](/sequence-files/IGVFFI7213YRKN/), [IGVFFI9766AIDX](/sequence-files/IGVFFI9766AIDX/), [IGVFFI2235HFZO](/sequence-files/IGVFFI2235HFZO/), [IGVFFI0585WOBD](/sequence-files/IGVFFI0585WOBD/), [IGVFFI0276GPEJ](/sequence-files/IGVFFI0276GPEJ/), [IGVFFI5980ZRCA](/sequence-files/IGVFFI5980ZRCA/) 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/IGVFDS1370QEJF/"
},
{
"category": "missing sequence specification",
"detail": "Measurement set [IGVFDS1370QEJF](/measurement-sets/IGVFDS1370QEJF/) has sequence file(s): [IGVFFI3324IWGH](/sequence-files/IGVFFI3324IWGH/), [IGVFFI6156DULO](/sequence-files/IGVFFI6156DULO/), [IGVFFI7213YRKN](/sequence-files/IGVFFI7213YRKN/), [IGVFFI9766AIDX](/sequence-files/IGVFFI9766AIDX/), [IGVFFI2235HFZO](/sequence-files/IGVFFI2235HFZO/), [IGVFFI0585WOBD](/sequence-files/IGVFFI0585WOBD/), [IGVFFI0276GPEJ](/sequence-files/IGVFFI0276GPEJ/), [IGVFFI5980ZRCA](/sequence-files/IGVFFI5980ZRCA/) 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/IGVFDS1370QEJF/"
},
{
"category": "mismatched status",
"detail": "Released in vitro system [IGVFSM2376QXPC](/in-vitro-systems/IGVFSM2376QXPC/) 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/IGVFSM2376QXPC/"
}
],
"WARNING": [
{
"category": "missing auxiliary set",
"detail": "Measurement set [IGVFDS1370QEJF](/measurement-sets/IGVFDS1370QEJF/) 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/IGVFDS1370QEJF/"
},
{
"category": "missing targeted genes",
"detail": "Measurement set [IGVFDS1370QEJF](/measurement-sets/IGVFDS1370QEJF/) 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/IGVFDS1370QEJF/"
}
]
},
"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": "2023-11-30T22:47:54.693800+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/IGVFFI3324IWGH/",
"accession": "IGVFFI3324IWGH",
"aliases": [
"jesse-engreitz:220829_8merInsertion-Jurkat_Stimulation-Amp_PPIF_promoter-BioRep1-FFrep2-FACS_Input-PCRrep1_R1"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2023-12-05T19:32:39.122425+00:00",
"file_format": "fastq",
"file_size": 7943605,
"href": "/sequence-files/IGVFFI3324IWGH/@@download/IGVFFI3324IWGH.fastq.gz",
"s3_uri": "s3://igvf-files/2023/12/05/9356ff3c-650c-4a1a-8585-2de5610d8f12/IGVFFI3324IWGH.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_S13-BioRep1-FFRep2-BinAll-PCRrep1_S126_R1_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI6156DULO/",
"accession": "IGVFFI6156DULO",
"aliases": [
"jesse-engreitz:220829_8merInsertion-Jurkat_Stimulation-Amp_PPIF_promoter-BioRep1-FFrep2-FACS_Input-PCRrep2_I2"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2023-12-05T20:31:01.514856+00:00",
"file_format": "fastq",
"file_size": 3474152,
"href": "/sequence-files/IGVFFI6156DULO/@@download/IGVFFI6156DULO.fastq.gz",
"s3_uri": "s3://igvf-files/2023/12/05/d07244b9-3c6f-43cb-8a04-4ba3a254122a/IGVFFI6156DULO.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_S13-BioRep1-FFRep2-BinAll-PCRrep2_S183_I2_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI7213YRKN/",
"accession": "IGVFFI7213YRKN",
"aliases": [
"jesse-engreitz:220829_8merInsertion-Jurkat_Stimulation-Amp_PPIF_promoter-BioRep1-FFrep2-FACS_Input-PCRrep1_I2"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2023-12-05T19:57:43.671827+00:00",
"file_format": "fastq",
"file_size": 3302685,
"href": "/sequence-files/IGVFFI7213YRKN/@@download/IGVFFI7213YRKN.fastq.gz",
"s3_uri": "s3://igvf-files/2023/12/05/03ec8a66-87b3-4a10-aeba-96d8351ab2fc/IGVFFI7213YRKN.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_S13-BioRep1-FFRep2-BinAll-PCRrep1_S126_I2_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI9766AIDX/",
"accession": "IGVFFI9766AIDX",
"aliases": [
"jesse-engreitz:220829_8merInsertion-Jurkat_Stimulation-Amp_PPIF_promoter-BioRep1-FFrep2-FACS_Input-PCRrep1_I1"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2023-12-05T19:49:35.652077+00:00",
"file_format": "fastq",
"file_size": 3336612,
"href": "/sequence-files/IGVFFI9766AIDX/@@download/IGVFFI9766AIDX.fastq.gz",
"s3_uri": "s3://igvf-files/2023/12/05/48a55b46-33a4-43dc-8fa9-3fa56282ad9c/IGVFFI9766AIDX.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_S13-BioRep1-FFRep2-BinAll-PCRrep1_S126_I1_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI2235HFZO/",
"accession": "IGVFFI2235HFZO",
"aliases": [
"jesse-engreitz:220829_8merInsertion-Jurkat_Stimulation-Amp_PPIF_promoter-BioRep1-FFrep2-FACS_Input-PCRrep2_I1"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2023-12-05T20:22:40.909763+00:00",
"file_format": "fastq",
"file_size": 3551949,
"href": "/sequence-files/IGVFFI2235HFZO/@@download/IGVFFI2235HFZO.fastq.gz",
"s3_uri": "s3://igvf-files/2023/12/05/0d7419e7-2dd4-4635-abf3-328e7129d775/IGVFFI2235HFZO.fastq.gz",
"sequencing_platform": {
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"status": "released",
"term_name": "Illumina NextSeq 550"
},
"status": "released",
"submitted_file_name": "220829_pPPIF_JurkatVFF-Jurkat-PE2A-BFP-pPPIF-Amp_pPPIF2_S13-BioRep1-FFRep2-BinAll-PCRrep2_S183_I1_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI0585WOBD/",
"accession": "IGVFFI0585WOBD",
"aliases": [
"jesse-engreitz:220829_8merInsertion-Jurkat_Stimulation-Amp_PPIF_promoter-BioRep1-FFrep2-FACS_Input-PCRrep2_R1"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2023-12-05T20:05:55.298338+00:00",
"file_format": "fastq",
"file_size": 8360796,
"href": "/sequence-files/IGVFFI0585WOBD/@@download/IGVFFI0585WOBD.fastq.gz",
"s3_uri": "s3://igvf-files/2023/12/05/7dfe9aa0-42fd-491a-97e8-7d7b65c87784/IGVFFI0585WOBD.fastq.gz",
"sequencing_platform": {
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"status": "released",
"term_name": "Illumina NextSeq 550"
},
"status": "released",
"submitted_file_name": "220829_pPPIF_JurkatVFF-Jurkat-PE2A-BFP-pPPIF-Amp_pPPIF2_S13-BioRep1-FFRep2-BinAll-PCRrep2_S183_R1_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI0276GPEJ/",
"accession": "IGVFFI0276GPEJ",
"aliases": [
"jesse-engreitz:220829_8merInsertion-Jurkat_Stimulation-Amp_PPIF_promoter-BioRep1-FFrep2-FACS_Input-PCRrep2_R2"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2023-12-05T20:14:14.260719+00:00",
"file_format": "fastq",
"file_size": 15663721,
"href": "/sequence-files/IGVFFI0276GPEJ/@@download/IGVFFI0276GPEJ.fastq.gz",
"s3_uri": "s3://igvf-files/2023/12/05/2298fd9c-b526-4da7-921f-72eea3e6c757/IGVFFI0276GPEJ.fastq.gz",
"sequencing_platform": {
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"status": "released",
"term_name": "Illumina NextSeq 550"
},
"status": "released",
"submitted_file_name": "220829_pPPIF_JurkatVFF-Jurkat-PE2A-BFP-pPPIF-Amp_pPPIF2_S13-BioRep1-FFRep2-BinAll-PCRrep2_S183_R2_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI5980ZRCA/",
"accession": "IGVFFI5980ZRCA",
"aliases": [
"jesse-engreitz:220829_8merInsertion-Jurkat_Stimulation-Amp_PPIF_promoter-BioRep1-FFrep2-FACS_Input-PCRrep1_R2"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2023-12-05T19:41:03.303699+00:00",
"file_format": "fastq",
"file_size": 14735320,
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"sequencing_platform": {
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"status": "released",
"term_name": "Illumina NextSeq 550"
},
"status": "released",
"submitted_file_name": "220829_pPPIF_JurkatVFF-Jurkat-PE2A-BFP-pPPIF-Amp_pPPIF2_S13-BioRep1-FFRep2-BinAll-PCRrep1_S126_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": "2023-12-20T23:05:04.107605+00:00",
"samples": [
{
"@id": "/in-vitro-systems/IGVFSM2376QXPC/",
"@type": [
"InVitroSystem",
"Biosample",
"Sample",
"Item"
],
"accession": "IGVFSM2376QXPC",
"aliases": [
"jesse-engreitz:220829_8merInsertion-Jurkat_Stimulation-Amp_PPIF_promoter-BioRep1-FFrep2-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": "2023-12-05T19:32:39.122425+00:00",
"summary": "unsorted FACS input CRISPR prime editing Variant-EFFECTS integrating a guide (sgRNA) library targeting sequence variants in a genomic locus",
"uuid": "9bccba93-4d77-4c6e-9319-4e006a96f912"
}