{
"@context": "/terms/",
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"@type": [
"MeasurementSet",
"FileSet",
"Item"
],
"accession": "IGVFDS7100AAFY",
"aliases": [
"jesse-engreitz:230523pPPIFEnformer-THP1-Amp_PPIF_promoter-BioRep2-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": "mismatched status",
"detail": "Released in vitro system [IGVFSM5250NIMK](/in-vitro-systems/IGVFSM5250NIMK/) 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/IGVFSM5250NIMK/"
},
{
"category": "missing sequencing kit",
"detail": "Measurement set [IGVFDS7100AAFY](/measurement-sets/IGVFDS7100AAFY/) has sequence file(s) [IGVFFI2512RPUJ](/sequence-files/IGVFFI2512RPUJ/), [IGVFFI9013CUKH](/sequence-files/IGVFFI9013CUKH/), [IGVFFI2065OIZT](/sequence-files/IGVFFI2065OIZT/), [IGVFFI9226GONZ](/sequence-files/IGVFFI9226GONZ/), [IGVFFI4911WJXN](/sequence-files/IGVFFI4911WJXN/), [IGVFFI8924EJNW](/sequence-files/IGVFFI8924EJNW/), [IGVFFI2324KTMM](/sequence-files/IGVFFI2324KTMM/), [IGVFFI4433NIDG](/sequence-files/IGVFFI4433NIDG/) 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/IGVFDS7100AAFY/"
},
{
"category": "missing sequence specification",
"detail": "Measurement set [IGVFDS7100AAFY](/measurement-sets/IGVFDS7100AAFY/) has sequence file(s): [IGVFFI2512RPUJ](/sequence-files/IGVFFI2512RPUJ/), [IGVFFI9013CUKH](/sequence-files/IGVFFI9013CUKH/), [IGVFFI2065OIZT](/sequence-files/IGVFFI2065OIZT/), [IGVFFI9226GONZ](/sequence-files/IGVFFI9226GONZ/), [IGVFFI4911WJXN](/sequence-files/IGVFFI4911WJXN/), [IGVFFI8924EJNW](/sequence-files/IGVFFI8924EJNW/), [IGVFFI2324KTMM](/sequence-files/IGVFFI2324KTMM/), [IGVFFI4433NIDG](/sequence-files/IGVFFI4433NIDG/) 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/IGVFDS7100AAFY/"
}
],
"WARNING": [
{
"category": "missing auxiliary set",
"detail": "Measurement set [IGVFDS7100AAFY](/measurement-sets/IGVFDS7100AAFY/) 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/IGVFDS7100AAFY/"
},
{
"category": "missing targeted genes",
"detail": "Measurement set [IGVFDS7100AAFY](/measurement-sets/IGVFDS7100AAFY/) 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/IGVFDS7100AAFY/"
}
]
},
"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"
},
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{
"@id": "/measurement-sets/IGVFDS5128CXIS/",
"accession": "IGVFDS5128CXIS",
"aliases": [
"jesse-engreitz:230523pPPIFEnformer-THP1-Amp_PPIF_promoter-THP1-PE2_Exp4_NegControl_AmpliconSequencing"
],
"status": "released"
}
],
"control_for": [],
"control_type": "unsorted FACS input",
"creation_timestamp": "2023-12-13T08:01:46.085940+00:00",
"donors": [
{
"@id": "/human-donors/IGVFDO7359LVPI/",
"accession": "IGVFDO7359LVPI",
"aliases": [
"igvf:donor_of_THP1"
],
"sex": "male",
"status": "released",
"taxa": "Homo sapiens"
}
],
"externally_hosted": false,
"file_set_type": "experimental data",
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{
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"accession": "IGVFFI2512RPUJ",
"aliases": [
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],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2023-12-13T16:44:21.902273+00:00",
"file_format": "fastq",
"file_size": 2048786,
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"s3_uri": "s3://igvf-files/2023/12/13/97af01d2-da26-4ca2-a5bd-facf0f1257f0/IGVFFI2512RPUJ.fastq.gz",
"sequencing_platform": {
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"status": "released",
"term_name": "Illumina NextSeq 550"
},
"status": "released",
"submitted_file_name": "230523pPPIFEnformerTHP1-THP1-PE-pPPIF_Enformer-Amp-pPPIF-BioRep2-FFRep2_BinAll-PCRrep1_S395_I2_001.fastq.gz",
"upload_status": "validated"
},
{
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"accession": "IGVFFI9013CUKH",
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"creation_timestamp": "2023-12-13T16:45:09.450815+00:00",
"file_format": "fastq",
"file_size": 2069257,
"href": "/sequence-files/IGVFFI9013CUKH/@@download/IGVFFI9013CUKH.fastq.gz",
"s3_uri": "s3://igvf-files/2023/12/13/989c62f1-7c6c-4e26-bf30-c2e86dc2190b/IGVFFI9013CUKH.fastq.gz",
"sequencing_platform": {
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"status": "released",
"term_name": "Illumina NextSeq 550"
},
"status": "released",
"submitted_file_name": "230523pPPIFEnformerTHP1-THP1-PE-pPPIF_Enformer-Amp-pPPIF-BioRep2-FFRep2_BinAll-PCRrep2_S396_I2_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI2065OIZT/",
"accession": "IGVFFI2065OIZT",
"aliases": [
"jesse-engreitz:230523pPPIFEnformer-THP1-Amp_PPIF_promoter-BioRep2-FFrep2-FACS_Input-PCRrep1_R2"
],
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"creation_timestamp": "2023-12-13T10:07:28.722821+00:00",
"file_format": "fastq",
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"href": "/sequence-files/IGVFFI2065OIZT/@@download/IGVFFI2065OIZT.fastq.gz",
"s3_uri": "s3://igvf-files/2023/12/13/c07246ca-4577-4929-b5f6-f8e291e4bae8/IGVFFI2065OIZT.fastq.gz",
"sequencing_platform": {
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"status": "released",
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},
"status": "released",
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"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI9226GONZ/",
"accession": "IGVFFI9226GONZ",
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],
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"controlled_access": false,
"creation_timestamp": "2023-12-13T10:08:22.722866+00:00",
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"href": "/sequence-files/IGVFFI9226GONZ/@@download/IGVFFI9226GONZ.fastq.gz",
"s3_uri": "s3://igvf-files/2023/12/13/77a5471f-62f7-42c5-be78-c99ae879d8bc/IGVFFI9226GONZ.fastq.gz",
"sequencing_platform": {
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"status": "released",
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},
"status": "released",
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"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI4911WJXN/",
"accession": "IGVFFI4911WJXN",
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"href": "/sequence-files/IGVFFI4911WJXN/@@download/IGVFFI4911WJXN.fastq.gz",
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"status": "released",
"term_name": "Illumina NextSeq 550"
},
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"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI8924EJNW/",
"accession": "IGVFFI8924EJNW",
"aliases": [
"jesse-engreitz:230523pPPIFEnformer-THP1-Amp_PPIF_promoter-BioRep2-FFrep2-FACS_Input-PCRrep1_R1"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2023-12-13T08:59:20.084883+00:00",
"file_format": "fastq",
"file_size": 9161446,
"href": "/sequence-files/IGVFFI8924EJNW/@@download/IGVFFI8924EJNW.fastq.gz",
"s3_uri": "s3://igvf-files/2023/12/13/f08f68ba-7611-42e2-8287-cf4fcf233841/IGVFFI8924EJNW.fastq.gz",
"sequencing_platform": {
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"status": "released",
"term_name": "Illumina NextSeq 550"
},
"status": "released",
"submitted_file_name": "230523pPPIFEnformerTHP1-THP1-PE-pPPIF_Enformer-Amp-pPPIF-BioRep2-FFRep2_BinAll-PCRrep1_S395_R1_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI2324KTMM/",
"accession": "IGVFFI2324KTMM",
"aliases": [
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],
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"controlled_access": false,
"creation_timestamp": "2023-12-13T15:41:26.649258+00:00",
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"term_name": "Illumina NextSeq 550"
},
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"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI4433NIDG/",
"accession": "IGVFFI4433NIDG",
"aliases": [
"jesse-engreitz:230523pPPIFEnformer-THP1-Amp_PPIF_promoter-BioRep2-FFrep2-FACS_Input-PCRrep2_R1"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2023-12-13T09:00:09.763376+00:00",
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},
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}
],
"input_for": [
"/analysis-sets/IGVFDS4359OODY/"
],
"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": "2023-12-20T23:07:24.024602+00:00",
"samples": [
{
"@id": "/in-vitro-systems/IGVFSM5250NIMK/",
"@type": [
"InVitroSystem",
"Biosample",
"Sample",
"Item"
],
"accession": "IGVFSM5250NIMK",
"aliases": [
"jesse-engreitz:230523pPPIFEnformer-THP1-Amp_PPIF_promoter-BioRep2-FFrep2-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_0001253/",
"@type": [
"SampleTerm",
"OntologyTerm",
"Item"
],
"aliases": [
"igvf:THP-1"
],
"status": "released",
"summary": "THP-1",
"term_name": "THP-1"
}
],
"status": "released",
"summary": "THP-1 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": "2023-12-13T08:59:20.084883+00:00",
"summary": "unsorted FACS input CRISPR prime editing Variant-EFFECTS integrating a guide (sgRNA) library targeting sequence variants in a genomic locus",
"uuid": "9976d83a-b3a4-4e75-ac13-5b7ff44a7c38"
}