{
"@context": "/terms/",
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"@type": [
"MeasurementSet",
"FileSet",
"Item"
],
"accession": "IGVFDS6266PDNX",
"aliases": [
"jesse-engreitz:230523pPPIFEnformer-THP1-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 [IGVFDS6266PDNX](/measurement-sets/IGVFDS6266PDNX/) has sequence file(s) [IGVFFI8725OZFM](/sequence-files/IGVFFI8725OZFM/), [IGVFFI3963AQTE](/sequence-files/IGVFFI3963AQTE/), [IGVFFI2132NUEI](/sequence-files/IGVFFI2132NUEI/), [IGVFFI7359ENGE](/sequence-files/IGVFFI7359ENGE/), [IGVFFI3861PWQJ](/sequence-files/IGVFFI3861PWQJ/), [IGVFFI6797EBWL](/sequence-files/IGVFFI6797EBWL/), [IGVFFI4529HCIO](/sequence-files/IGVFFI4529HCIO/), [IGVFFI1575DPTU](/sequence-files/IGVFFI1575DPTU/) 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/IGVFDS6266PDNX/"
},
{
"category": "missing sequence specification",
"detail": "Measurement set [IGVFDS6266PDNX](/measurement-sets/IGVFDS6266PDNX/) has sequence file(s): [IGVFFI8725OZFM](/sequence-files/IGVFFI8725OZFM/), [IGVFFI3963AQTE](/sequence-files/IGVFFI3963AQTE/), [IGVFFI2132NUEI](/sequence-files/IGVFFI2132NUEI/), [IGVFFI7359ENGE](/sequence-files/IGVFFI7359ENGE/), [IGVFFI3861PWQJ](/sequence-files/IGVFFI3861PWQJ/), [IGVFFI6797EBWL](/sequence-files/IGVFFI6797EBWL/), [IGVFFI4529HCIO](/sequence-files/IGVFFI4529HCIO/), [IGVFFI1575DPTU](/sequence-files/IGVFFI1575DPTU/) 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/IGVFDS6266PDNX/"
},
{
"category": "mismatched status",
"detail": "Released in vitro system [IGVFSM8731UBTA](/in-vitro-systems/IGVFSM8731UBTA/) 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/IGVFSM8731UBTA/"
}
],
"WARNING": [
{
"category": "missing auxiliary set",
"detail": "Measurement set [IGVFDS6266PDNX](/measurement-sets/IGVFDS6266PDNX/) 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/IGVFDS6266PDNX/"
},
{
"category": "missing targeted genes",
"detail": "Measurement set [IGVFDS6266PDNX](/measurement-sets/IGVFDS6266PDNX/) 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/IGVFDS6266PDNX/"
}
]
},
"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": "2023-12-13T08:01:39.629694+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": "IGVFFI8725OZFM",
"aliases": [
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],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2023-12-13T09:33:24.863698+00:00",
"file_format": "fastq",
"file_size": 11909630,
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"s3_uri": "s3://igvf-files/2023/12/13/6994c765-b524-4408-9ceb-63facc11f3bf/IGVFFI8725OZFM.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-BioRep1-FFRep2_BinAll-PCRrep1_S387_R2_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI3963AQTE/",
"accession": "IGVFFI3963AQTE",
"aliases": [
"jesse-engreitz:230523pPPIFEnformer-THP1-Amp_PPIF_promoter-BioRep1-FFrep2-FACS_Input-PCRrep2_R1"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2023-12-13T08:26:41.565445+00:00",
"file_format": "fastq",
"file_size": 9898836,
"href": "/sequence-files/IGVFFI3963AQTE/@@download/IGVFFI3963AQTE.fastq.gz",
"s3_uri": "s3://igvf-files/2023/12/13/23340fb6-1999-4768-a9ec-f7bbbd67dd2a/IGVFFI3963AQTE.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-BioRep1-FFRep2_BinAll-PCRrep2_S388_R1_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI2132NUEI/",
"accession": "IGVFFI2132NUEI",
"aliases": [
"jesse-engreitz:230523pPPIFEnformer-THP1-Amp_PPIF_promoter-BioRep1-FFrep2-FACS_Input-PCRrep2_I2"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2023-12-13T16:13:28.394690+00:00",
"file_format": "fastq",
"file_size": 2229669,
"href": "/sequence-files/IGVFFI2132NUEI/@@download/IGVFFI2132NUEI.fastq.gz",
"s3_uri": "s3://igvf-files/2023/12/13/02773513-0604-43e7-8f41-461076dad164/IGVFFI2132NUEI.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-BioRep1-FFRep2_BinAll-PCRrep2_S388_I2_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI7359ENGE/",
"accession": "IGVFFI7359ENGE",
"aliases": [
"jesse-engreitz:230523pPPIFEnformer-THP1-Amp_PPIF_promoter-BioRep1-FFrep2-FACS_Input-PCRrep1_I1"
],
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"controlled_access": false,
"creation_timestamp": "2023-12-13T15:08:57.515294+00:00",
"file_format": "fastq",
"file_size": 2072123,
"href": "/sequence-files/IGVFFI7359ENGE/@@download/IGVFFI7359ENGE.fastq.gz",
"s3_uri": "s3://igvf-files/2023/12/13/414bcba3-4595-4dc6-8378-c2259215b434/IGVFFI7359ENGE.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-BioRep1-FFRep2_BinAll-PCRrep1_S387_I1_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI3861PWQJ/",
"accession": "IGVFFI3861PWQJ",
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"jesse-engreitz:230523pPPIFEnformer-THP1-Amp_PPIF_promoter-BioRep1-FFrep2-FACS_Input-PCRrep2_I1"
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"controlled_access": false,
"creation_timestamp": "2023-12-13T15:09:44.818029+00:00",
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"href": "/sequence-files/IGVFFI3861PWQJ/@@download/IGVFFI3861PWQJ.fastq.gz",
"s3_uri": "s3://igvf-files/2023/12/13/78a515e4-8820-46df-93ad-c07c15307f4d/IGVFFI3861PWQJ.fastq.gz",
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"term_name": "Illumina NextSeq 550"
},
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"submitted_file_name": "230523pPPIFEnformerTHP1-THP1-PE-pPPIF_Enformer-Amp-pPPIF-BioRep1-FFRep2_BinAll-PCRrep2_S388_I1_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI6797EBWL/",
"accession": "IGVFFI6797EBWL",
"aliases": [
"jesse-engreitz:230523pPPIFEnformer-THP1-Amp_PPIF_promoter-BioRep1-FFrep2-FACS_Input-PCRrep2_R2"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2023-12-13T09:34:14.351899+00:00",
"file_format": "fastq",
"file_size": 12378660,
"href": "/sequence-files/IGVFFI6797EBWL/@@download/IGVFFI6797EBWL.fastq.gz",
"s3_uri": "s3://igvf-files/2023/12/13/7c9a1ebc-96eb-4c6c-8f5e-3ecc8da2c6a5/IGVFFI6797EBWL.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-BioRep1-FFRep2_BinAll-PCRrep2_S388_R2_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI4529HCIO/",
"accession": "IGVFFI4529HCIO",
"aliases": [
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"creation_timestamp": "2023-12-13T16:12:40.860206+00:00",
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"status": "released",
"term_name": "Illumina NextSeq 550"
},
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"submitted_file_name": "230523pPPIFEnformerTHP1-THP1-PE-pPPIF_Enformer-Amp-pPPIF-BioRep1-FFRep2_BinAll-PCRrep1_S387_I2_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI1575DPTU/",
"accession": "IGVFFI1575DPTU",
"aliases": [
"jesse-engreitz:230523pPPIFEnformer-THP1-Amp_PPIF_promoter-BioRep1-FFrep2-FACS_Input-PCRrep1_R1"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2023-12-13T08:25:51.715454+00:00",
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"status": "released",
"term_name": "Illumina NextSeq 550"
},
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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": "2023-12-20T23:08:05.657905+00:00",
"samples": [
{
"@id": "/in-vitro-systems/IGVFSM8731UBTA/",
"@type": [
"InVitroSystem",
"Biosample",
"Sample",
"Item"
],
"accession": "IGVFSM8731UBTA",
"aliases": [
"jesse-engreitz:230523pPPIFEnformer-THP1-Amp_PPIF_promoter-BioRep1-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": "2023-12-13T08:25:51.715454+00:00",
"summary": "unsorted FACS input CRISPR prime editing Variant-EFFECTS integrating a guide (sgRNA) library targeting sequence variants in a genomic locus",
"uuid": "0f6aa383-c8c7-48ab-8da5-b564c5fbec85"
}