{
"@context": "/terms/",
"@id": "/measurement-sets/IGVFDS7480YPZN/",
"@type": [
"MeasurementSet",
"FileSet",
"Item"
],
"accession": "IGVFDS7480YPZN",
"aliases": [
"jesse-engreitz:230423pPPIFEnformer-Jurkat-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 [IGVFSM9783LUAL](/in-vitro-systems/IGVFSM9783LUAL/) has in progress subobject construct library set [IGVFDS2385DHZO](/construct-library-sets/IGVFDS2385DHZO/).",
"level": 30,
"level_name": "INTERNAL_ACTION",
"name": "audit_item_status",
"path": "/in-vitro-systems/IGVFSM9783LUAL/"
},
{
"category": "missing sequencing kit",
"detail": "Measurement set [IGVFDS7480YPZN](/measurement-sets/IGVFDS7480YPZN/) has sequence file(s) [IGVFFI2233RWNR](/sequence-files/IGVFFI2233RWNR/), [IGVFFI5279HUDA](/sequence-files/IGVFFI5279HUDA/), [IGVFFI8006HWOO](/sequence-files/IGVFFI8006HWOO/), [IGVFFI2156OWVS](/sequence-files/IGVFFI2156OWVS/), [IGVFFI7494WYGV](/sequence-files/IGVFFI7494WYGV/), [IGVFFI6177QUPZ](/sequence-files/IGVFFI6177QUPZ/), [IGVFFI9655SHHZ](/sequence-files/IGVFFI9655SHHZ/), [IGVFFI5360SYEL](/sequence-files/IGVFFI5360SYEL/) 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/IGVFDS7480YPZN/"
},
{
"category": "missing sequence specification",
"detail": "Measurement set [IGVFDS7480YPZN](/measurement-sets/IGVFDS7480YPZN/) has sequence file(s): [IGVFFI2233RWNR](/sequence-files/IGVFFI2233RWNR/), [IGVFFI5279HUDA](/sequence-files/IGVFFI5279HUDA/), [IGVFFI8006HWOO](/sequence-files/IGVFFI8006HWOO/), [IGVFFI2156OWVS](/sequence-files/IGVFFI2156OWVS/), [IGVFFI7494WYGV](/sequence-files/IGVFFI7494WYGV/), [IGVFFI6177QUPZ](/sequence-files/IGVFFI6177QUPZ/), [IGVFFI9655SHHZ](/sequence-files/IGVFFI9655SHHZ/), [IGVFFI5360SYEL](/sequence-files/IGVFFI5360SYEL/) 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/IGVFDS7480YPZN/"
}
],
"WARNING": [
{
"category": "missing auxiliary set",
"detail": "Measurement set [IGVFDS7480YPZN](/measurement-sets/IGVFDS7480YPZN/) 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/IGVFDS7480YPZN/"
},
{
"category": "missing targeted genes",
"detail": "Measurement set [IGVFDS7480YPZN](/measurement-sets/IGVFDS7480YPZN/) 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/IGVFDS7480YPZN/"
}
]
},
"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/IGVFDS4869FXYY/",
"accession": "IGVFDS4869FXYY",
"aliases": [
"jesse-engreitz:230423pPPIFEnformer-Jurkat-Amp_PPIF_promoter-Jurkat-PE2_Exp2_NegControl_AmpliconSequencing"
],
"status": "released"
}
],
"control_for": [],
"control_type": "unsorted FACS input",
"creation_timestamp": "2023-12-13T08:48:04.013457+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": [
{
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"accession": "IGVFFI2233RWNR",
"aliases": [
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"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2023-12-13T09:28:50.562466+00:00",
"file_format": "fastq",
"file_size": 6090790,
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"s3_uri": "s3://igvf-files/2023/12/13/24e920e6-ebf1-4570-a7ac-a0e3732ef4c7/IGVFFI2233RWNR.fastq.gz",
"sequencing_platform": {
"@id": "/platform-terms/EFO_0008566/",
"status": "released",
"term_name": "Illumina NextSeq 550"
},
"status": "released",
"submitted_file_name": "230423pPPIFEnformerJurkat-Jurkat-PE-pPPIF_Enformer-Amp-pPPIF-BioRep1-FFRep1_BinAll-PCRrep1_S385_R1_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI5279HUDA/",
"accession": "IGVFFI5279HUDA",
"aliases": [
"jesse-engreitz:230423pPPIFEnformer-Jurkat-Amp_PPIF_promoter-BioRep1-FFrep1-FACS_Input-PCRrep2_I2"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2023-12-13T16:06:43.832723+00:00",
"file_format": "fastq",
"file_size": 1938173,
"href": "/sequence-files/IGVFFI5279HUDA/@@download/IGVFFI5279HUDA.fastq.gz",
"s3_uri": "s3://igvf-files/2023/12/13/04830ecf-618f-4418-88c1-cfc1854c89b0/IGVFFI5279HUDA.fastq.gz",
"sequencing_platform": {
"@id": "/platform-terms/EFO_0008566/",
"status": "released",
"term_name": "Illumina NextSeq 550"
},
"status": "released",
"submitted_file_name": "230423pPPIFEnformerJurkat-Jurkat-PE-pPPIF_Enformer-Amp-pPPIF-BioRep1-FFRep1_BinAll-PCRrep2_S386_I2_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI8006HWOO/",
"accession": "IGVFFI8006HWOO",
"aliases": [
"jesse-engreitz:230423pPPIFEnformer-Jurkat-Amp_PPIF_promoter-BioRep1-FFrep1-FACS_Input-PCRrep2_R2"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2023-12-13T10:34:11.908432+00:00",
"file_format": "fastq",
"file_size": 9436864,
"href": "/sequence-files/IGVFFI8006HWOO/@@download/IGVFFI8006HWOO.fastq.gz",
"s3_uri": "s3://igvf-files/2023/12/13/8276e022-0008-4f3f-b8f0-4e46aacf925a/IGVFFI8006HWOO.fastq.gz",
"sequencing_platform": {
"@id": "/platform-terms/EFO_0008566/",
"status": "released",
"term_name": "Illumina NextSeq 550"
},
"status": "released",
"submitted_file_name": "230423pPPIFEnformerJurkat-Jurkat-PE-pPPIF_Enformer-Amp-pPPIF-BioRep1-FFRep1_BinAll-PCRrep2_S386_R2_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI2156OWVS/",
"accession": "IGVFFI2156OWVS",
"aliases": [
"jesse-engreitz:230423pPPIFEnformer-Jurkat-Amp_PPIF_promoter-BioRep1-FFrep1-FACS_Input-PCRrep2_I1"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2023-12-13T15:03:56.438664+00:00",
"file_format": "fastq",
"file_size": 1901338,
"href": "/sequence-files/IGVFFI2156OWVS/@@download/IGVFFI2156OWVS.fastq.gz",
"s3_uri": "s3://igvf-files/2023/12/13/98fc13ba-44fa-41a7-b601-0e411da551f4/IGVFFI2156OWVS.fastq.gz",
"sequencing_platform": {
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"status": "released",
"term_name": "Illumina NextSeq 550"
},
"status": "released",
"submitted_file_name": "230423pPPIFEnformerJurkat-Jurkat-PE-pPPIF_Enformer-Amp-pPPIF-BioRep1-FFRep1_BinAll-PCRrep2_S386_I1_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI7494WYGV/",
"accession": "IGVFFI7494WYGV",
"aliases": [
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],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2023-12-13T10:33:09.474241+00:00",
"file_format": "fastq",
"file_size": 8383459,
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"s3_uri": "s3://igvf-files/2023/12/13/348bfc55-5b30-4017-b1e5-4a6907c1b06f/IGVFFI7494WYGV.fastq.gz",
"sequencing_platform": {
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"status": "released",
"term_name": "Illumina NextSeq 550"
},
"status": "released",
"submitted_file_name": "230423pPPIFEnformerJurkat-Jurkat-PE-pPPIF_Enformer-Amp-pPPIF-BioRep1-FFRep1_BinAll-PCRrep1_S385_R2_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI6177QUPZ/",
"accession": "IGVFFI6177QUPZ",
"aliases": [
"jesse-engreitz:230423pPPIFEnformer-Jurkat-Amp_PPIF_promoter-BioRep1-FFrep1-FACS_Input-PCRrep1_I1"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2023-12-13T15:03:00.670266+00:00",
"file_format": "fastq",
"file_size": 1673359,
"href": "/sequence-files/IGVFFI6177QUPZ/@@download/IGVFFI6177QUPZ.fastq.gz",
"s3_uri": "s3://igvf-files/2023/12/13/65b67d1d-c879-4b53-aa1e-3311f5e43e2f/IGVFFI6177QUPZ.fastq.gz",
"sequencing_platform": {
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"status": "released",
"term_name": "Illumina NextSeq 550"
},
"status": "released",
"submitted_file_name": "230423pPPIFEnformerJurkat-Jurkat-PE-pPPIF_Enformer-Amp-pPPIF-BioRep1-FFRep1_BinAll-PCRrep1_S385_I1_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI9655SHHZ/",
"accession": "IGVFFI9655SHHZ",
"aliases": [
"jesse-engreitz:230423pPPIFEnformer-Jurkat-Amp_PPIF_promoter-BioRep1-FFrep1-FACS_Input-PCRrep2_R1"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2023-12-13T09:29:48.614547+00:00",
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"file_size": 6862384,
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"sequencing_platform": {
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"status": "released",
"term_name": "Illumina NextSeq 550"
},
"status": "released",
"submitted_file_name": "230423pPPIFEnformerJurkat-Jurkat-PE-pPPIF_Enformer-Amp-pPPIF-BioRep1-FFRep1_BinAll-PCRrep2_S386_R1_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI5360SYEL/",
"accession": "IGVFFI5360SYEL",
"aliases": [
"jesse-engreitz:230423pPPIFEnformer-Jurkat-Amp_PPIF_promoter-BioRep1-FFrep1-FACS_Input-PCRrep1_I2"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2023-12-13T16:05:46.158314+00:00",
"file_format": "fastq",
"file_size": 1717806,
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"sequencing_platform": {
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"status": "released",
"term_name": "Illumina NextSeq 550"
},
"status": "released",
"submitted_file_name": "230423pPPIFEnformerJurkat-Jurkat-PE-pPPIF_Enformer-Amp-pPPIF-BioRep1-FFRep1_BinAll-PCRrep1_S385_I2_001.fastq.gz",
"upload_status": "validated"
}
],
"input_for": [
"/analysis-sets/IGVFDS6299IJHG/"
],
"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": "2023-12-20T23:08:51.860965+00:00",
"samples": [
{
"@id": "/in-vitro-systems/IGVFSM9783LUAL/",
"@type": [
"InVitroSystem",
"Biosample",
"Sample",
"Item"
],
"accession": "IGVFSM9783LUAL",
"aliases": [
"jesse-engreitz:230423pPPIFEnformer-Jurkat-Amp_PPIF_promoter-BioRep1-FFrep1-FACS_Input"
],
"classifications": [
"cell line"
],
"construct_library_sets": [
{
"@id": "/construct-library-sets/IGVFDS2385DHZO/",
"accession": "IGVFDS2385DHZO",
"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 modified with CRISPR prime editing Sp-nCas9-M-MLV RT (PE2), transfected with a guide library",
"taxa": "Homo sapiens"
}
],
"schema_version": "23",
"status": "released",
"submitted_by": {
"@id": "/users/f9e7cd82-a407-4a20-89ee-f4dc668b0cbe/",
"title": "Michael Montgomery"
},
"submitted_files_timestamp": "2023-12-13T09:28:50.562466+00:00",
"summary": "unsorted FACS input CRISPR prime editing Variant-EFFECTS integrating a guide (sgRNA) library targeting sequence variants in a genomic locus",
"uuid": "d1d6217c-5fbe-416a-81d4-bff091527407"
}