{
"@context": "/terms/",
"@id": "/measurement-sets/IGVFDS2294QFQV/",
"@type": [
"MeasurementSet",
"FileSet",
"Item"
],
"accession": "IGVFDS2294QFQV",
"aliases": [
"jesse-engreitz:230523pPPIFEnformer-THP1-Amp_PPIF_promoter-BioRep2-FFrep3-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 [IGVFDS2294QFQV](/measurement-sets/IGVFDS2294QFQV/) has sequence file(s) [IGVFFI1568WAJV](/sequence-files/IGVFFI1568WAJV/), [IGVFFI8823EBJO](/sequence-files/IGVFFI8823EBJO/), [IGVFFI2671WOEH](/sequence-files/IGVFFI2671WOEH/), [IGVFFI2442QEWF](/sequence-files/IGVFFI2442QEWF/), [IGVFFI9963VRYP](/sequence-files/IGVFFI9963VRYP/), [IGVFFI9805KWPC](/sequence-files/IGVFFI9805KWPC/), [IGVFFI3319FOYH](/sequence-files/IGVFFI3319FOYH/), [IGVFFI3911TJMQ](/sequence-files/IGVFFI3911TJMQ/) 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/IGVFDS2294QFQV/"
},
{
"category": "missing sequence specification",
"detail": "Measurement set [IGVFDS2294QFQV](/measurement-sets/IGVFDS2294QFQV/) has sequence file(s): [IGVFFI1568WAJV](/sequence-files/IGVFFI1568WAJV/), [IGVFFI8823EBJO](/sequence-files/IGVFFI8823EBJO/), [IGVFFI2671WOEH](/sequence-files/IGVFFI2671WOEH/), [IGVFFI2442QEWF](/sequence-files/IGVFFI2442QEWF/), [IGVFFI9963VRYP](/sequence-files/IGVFFI9963VRYP/), [IGVFFI9805KWPC](/sequence-files/IGVFFI9805KWPC/), [IGVFFI3319FOYH](/sequence-files/IGVFFI3319FOYH/), [IGVFFI3911TJMQ](/sequence-files/IGVFFI3911TJMQ/) 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/IGVFDS2294QFQV/"
},
{
"category": "mismatched status",
"detail": "Released in vitro system [IGVFSM6859MCDG](/in-vitro-systems/IGVFSM6859MCDG/) 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/IGVFSM6859MCDG/"
}
],
"WARNING": [
{
"category": "missing auxiliary set",
"detail": "Measurement set [IGVFDS2294QFQV](/measurement-sets/IGVFDS2294QFQV/) 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/IGVFDS2294QFQV/"
},
{
"category": "missing targeted genes",
"detail": "Measurement set [IGVFDS2294QFQV](/measurement-sets/IGVFDS2294QFQV/) 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/IGVFDS2294QFQV/"
}
]
},
"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/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": "2023-12-13T08:01:47.544384+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",
"files": [
{
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"accession": "IGVFFI1568WAJV",
"aliases": [
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],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2023-12-13T10:15:59.715803+00:00",
"file_format": "fastq",
"file_size": 12053449,
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"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-FFRep3_BinAll-PCRrep1_S397_R2_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI8823EBJO/",
"accession": "IGVFFI8823EBJO",
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"jesse-engreitz:230523pPPIFEnformer-THP1-Amp_PPIF_promoter-BioRep2-FFrep3-FACS_Input-PCRrep2_R1"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2023-12-13T09:08:34.448431+00:00",
"file_format": "fastq",
"file_size": 9472446,
"href": "/sequence-files/IGVFFI8823EBJO/@@download/IGVFFI8823EBJO.fastq.gz",
"s3_uri": "s3://igvf-files/2023/12/13/6869023f-da81-4798-b99d-938b96356ef8/IGVFFI8823EBJO.fastq.gz",
"sequencing_platform": {
"@id": "/platform-terms/EFO_0008566/",
"status": "released",
"term_name": "Illumina NextSeq 550"
},
"status": "released",
"submitted_file_name": "230523pPPIFEnformerTHP1-THP1-PE-pPPIF_Enformer-Amp-pPPIF-BioRep2-FFRep3_BinAll-PCRrep2_S398_R1_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI2671WOEH/",
"accession": "IGVFFI2671WOEH",
"aliases": [
"jesse-engreitz:230523pPPIFEnformer-THP1-Amp_PPIF_promoter-BioRep2-FFrep3-FACS_Input-PCRrep2_I1"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2023-12-13T15:49:21.490992+00:00",
"file_format": "fastq",
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"href": "/sequence-files/IGVFFI2671WOEH/@@download/IGVFFI2671WOEH.fastq.gz",
"s3_uri": "s3://igvf-files/2023/12/13/ea5292b8-50d6-4061-adcb-532f242977b7/IGVFFI2671WOEH.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-FFRep3_BinAll-PCRrep2_S398_I1_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI2442QEWF/",
"accession": "IGVFFI2442QEWF",
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"jesse-engreitz:230523pPPIFEnformer-THP1-Amp_PPIF_promoter-BioRep2-FFrep3-FACS_Input-PCRrep1_I1"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2023-12-13T15:48:33.049196+00:00",
"file_format": "fastq",
"file_size": 2249923,
"href": "/sequence-files/IGVFFI2442QEWF/@@download/IGVFFI2442QEWF.fastq.gz",
"s3_uri": "s3://igvf-files/2023/12/13/1e470a26-5ae4-415b-b120-dff41d7b5ff6/IGVFFI2442QEWF.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-FFRep3_BinAll-PCRrep1_S397_I1_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI9963VRYP/",
"accession": "IGVFFI9963VRYP",
"aliases": [
"jesse-engreitz:230523pPPIFEnformer-THP1-Amp_PPIF_promoter-BioRep2-FFrep3-FACS_Input-PCRrep2_I2"
],
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"controlled_access": false,
"creation_timestamp": "2023-12-13T16:53:18.981137+00:00",
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"href": "/sequence-files/IGVFFI9963VRYP/@@download/IGVFFI9963VRYP.fastq.gz",
"s3_uri": "s3://igvf-files/2023/12/13/4f2e8a97-342c-4a80-85c2-da47348ceccb/IGVFFI9963VRYP.fastq.gz",
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"status": "released",
"term_name": "Illumina NextSeq 550"
},
"status": "released",
"submitted_file_name": "230523pPPIFEnformerTHP1-THP1-PE-pPPIF_Enformer-Amp-pPPIF-BioRep2-FFRep3_BinAll-PCRrep2_S398_I2_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI9805KWPC/",
"accession": "IGVFFI9805KWPC",
"aliases": [
"jesse-engreitz:230523pPPIFEnformer-THP1-Amp_PPIF_promoter-BioRep2-FFrep3-FACS_Input-PCRrep1_I2"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2023-12-13T16:52:31.378697+00:00",
"file_format": "fastq",
"file_size": 2128460,
"href": "/sequence-files/IGVFFI9805KWPC/@@download/IGVFFI9805KWPC.fastq.gz",
"s3_uri": "s3://igvf-files/2023/12/13/4d5bc3e5-40f1-4e2c-934e-ffb05a6485da/IGVFFI9805KWPC.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-FFRep3_BinAll-PCRrep1_S397_I2_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI3319FOYH/",
"accession": "IGVFFI3319FOYH",
"aliases": [
"jesse-engreitz:230523pPPIFEnformer-THP1-Amp_PPIF_promoter-BioRep2-FFrep3-FACS_Input-PCRrep2_R2"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2023-12-13T10:16:49.880681+00:00",
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"status": "released",
"term_name": "Illumina NextSeq 550"
},
"status": "released",
"submitted_file_name": "230523pPPIFEnformerTHP1-THP1-PE-pPPIF_Enformer-Amp-pPPIF-BioRep2-FFRep3_BinAll-PCRrep2_S398_R2_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI3911TJMQ/",
"accession": "IGVFFI3911TJMQ",
"aliases": [
"jesse-engreitz:230523pPPIFEnformer-THP1-Amp_PPIF_promoter-BioRep2-FFrep3-FACS_Input-PCRrep1_R1"
],
"content_type": "reads",
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"creation_timestamp": "2023-12-13T09:07:44.310137+00:00",
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"sequencing_platform": {
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},
"status": "released",
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"upload_status": "validated"
}
],
"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": "2023-12-20T23:07:12.309741+00:00",
"samples": [
{
"@id": "/in-vitro-systems/IGVFSM6859MCDG/",
"@type": [
"InVitroSystem",
"Biosample",
"Sample",
"Item"
],
"accession": "IGVFSM6859MCDG",
"aliases": [
"jesse-engreitz:230523pPPIFEnformer-THP1-Amp_PPIF_promoter-BioRep2-FFrep3-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": "2023-12-13T09:07:44.310137+00:00",
"summary": "unsorted FACS input CRISPR prime editing Variant-EFFECTS integrating a guide (sgRNA) library targeting sequence variants in a genomic locus",
"uuid": "6bc02357-7b38-46ed-8ec5-32170b618395"
}