{
"@context": "/terms/",
"@id": "/measurement-sets/IGVFDS2337XGGI/",
"@type": [
"MeasurementSet",
"FileSet",
"Item"
],
"accession": "IGVFDS2337XGGI",
"aliases": [
"jesse-engreitz:230523pPPIFEnformer-THP1-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": "missing sequencing kit",
"detail": "Measurement set [IGVFDS2337XGGI](/measurement-sets/IGVFDS2337XGGI/) has sequence file(s) [IGVFFI3413AAZK](/sequence-files/IGVFFI3413AAZK/), [IGVFFI2477GMGG](/sequence-files/IGVFFI2477GMGG/), [IGVFFI0286YAHE](/sequence-files/IGVFFI0286YAHE/), [IGVFFI6808ADCB](/sequence-files/IGVFFI6808ADCB/), [IGVFFI8618ZBHF](/sequence-files/IGVFFI8618ZBHF/), [IGVFFI8759ZLLM](/sequence-files/IGVFFI8759ZLLM/), [IGVFFI5182ZRIW](/sequence-files/IGVFFI5182ZRIW/), [IGVFFI4701UFRL](/sequence-files/IGVFFI4701UFRL/) 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/IGVFDS2337XGGI/"
},
{
"category": "missing sequence specification",
"detail": "Measurement set [IGVFDS2337XGGI](/measurement-sets/IGVFDS2337XGGI/) has sequence file(s): [IGVFFI3413AAZK](/sequence-files/IGVFFI3413AAZK/), [IGVFFI2477GMGG](/sequence-files/IGVFFI2477GMGG/), [IGVFFI0286YAHE](/sequence-files/IGVFFI0286YAHE/), [IGVFFI6808ADCB](/sequence-files/IGVFFI6808ADCB/), [IGVFFI8618ZBHF](/sequence-files/IGVFFI8618ZBHF/), [IGVFFI8759ZLLM](/sequence-files/IGVFFI8759ZLLM/), [IGVFFI5182ZRIW](/sequence-files/IGVFFI5182ZRIW/), [IGVFFI4701UFRL](/sequence-files/IGVFFI4701UFRL/) 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/IGVFDS2337XGGI/"
},
{
"category": "mismatched status",
"detail": "Released in vitro system [IGVFSM0390WQRT](/in-vitro-systems/IGVFSM0390WQRT/) 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/IGVFSM0390WQRT/"
}
],
"WARNING": [
{
"category": "missing auxiliary set",
"detail": "Measurement set [IGVFDS2337XGGI](/measurement-sets/IGVFDS2337XGGI/) 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/IGVFDS2337XGGI/"
},
{
"category": "missing targeted genes",
"detail": "Measurement set [IGVFDS2337XGGI](/measurement-sets/IGVFDS2337XGGI/) 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/IGVFDS2337XGGI/"
}
]
},
"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": "2023-12-13T08:01:37.781351+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": "IGVFFI3413AAZK",
"aliases": [
"jesse-engreitz:230523pPPIFEnformer-THP1-Amp_PPIF_promoter-BioRep1-FFrep1-FACS_Input-PCRrep1_R2"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2023-12-13T09:24:44.985355+00:00",
"file_format": "fastq",
"file_size": 11891551,
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"s3_uri": "s3://igvf-files/2023/12/13/20b68179-021e-48cb-9644-99a055f36f75/IGVFFI3413AAZK.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-FFRep1_BinAll-PCRrep1_S385_R2_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI2477GMGG/",
"accession": "IGVFFI2477GMGG",
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"jesse-engreitz:230523pPPIFEnformer-THP1-Amp_PPIF_promoter-BioRep1-FFrep1-FACS_Input-PCRrep1_R1"
],
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"controlled_access": false,
"creation_timestamp": "2023-12-13T08:17:09.400088+00:00",
"file_format": "fastq",
"file_size": 9479496,
"href": "/sequence-files/IGVFFI2477GMGG/@@download/IGVFFI2477GMGG.fastq.gz",
"s3_uri": "s3://igvf-files/2023/12/13/b80f380b-e36e-4ba3-945d-00f105299f7c/IGVFFI2477GMGG.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-FFRep1_BinAll-PCRrep1_S385_R1_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI0286YAHE/",
"accession": "IGVFFI0286YAHE",
"aliases": [
"jesse-engreitz:230523pPPIFEnformer-THP1-Amp_PPIF_promoter-BioRep1-FFrep1-FACS_Input-PCRrep2_I1"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2023-12-13T15:01:35.807128+00:00",
"file_format": "fastq",
"file_size": 2133872,
"href": "/sequence-files/IGVFFI0286YAHE/@@download/IGVFFI0286YAHE.fastq.gz",
"s3_uri": "s3://igvf-files/2023/12/13/f3a83b69-0275-4bd4-b366-286ab82ffd17/IGVFFI0286YAHE.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-FFRep1_BinAll-PCRrep2_S386_I1_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI6808ADCB/",
"accession": "IGVFFI6808ADCB",
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],
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"controlled_access": false,
"creation_timestamp": "2023-12-13T16:04:23.157166+00:00",
"file_format": "fastq",
"file_size": 2121700,
"href": "/sequence-files/IGVFFI6808ADCB/@@download/IGVFFI6808ADCB.fastq.gz",
"s3_uri": "s3://igvf-files/2023/12/13/cf744e73-48e9-498a-a62b-3958abdd5ac5/IGVFFI6808ADCB.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-FFRep1_BinAll-PCRrep1_S385_I2_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI8618ZBHF/",
"accession": "IGVFFI8618ZBHF",
"aliases": [
"jesse-engreitz:230523pPPIFEnformer-THP1-Amp_PPIF_promoter-BioRep1-FFrep1-FACS_Input-PCRrep2_R1"
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"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2023-12-13T08:18:08.950302+00:00",
"file_format": "fastq",
"file_size": 9634269,
"href": "/sequence-files/IGVFFI8618ZBHF/@@download/IGVFFI8618ZBHF.fastq.gz",
"s3_uri": "s3://igvf-files/2023/12/13/5718f589-a432-4335-9878-23c90b7abc48/IGVFFI8618ZBHF.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-FFRep1_BinAll-PCRrep2_S386_R1_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI8759ZLLM/",
"accession": "IGVFFI8759ZLLM",
"aliases": [
"jesse-engreitz:230523pPPIFEnformer-THP1-Amp_PPIF_promoter-BioRep1-FFrep1-FACS_Input-PCRrep1_I1"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2023-12-13T15:00:38.641222+00:00",
"file_format": "fastq",
"file_size": 2066926,
"href": "/sequence-files/IGVFFI8759ZLLM/@@download/IGVFFI8759ZLLM.fastq.gz",
"s3_uri": "s3://igvf-files/2023/12/13/bd2e3fa8-3e3c-443b-8404-f77fd71652f8/IGVFFI8759ZLLM.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-FFRep1_BinAll-PCRrep1_S385_I1_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI5182ZRIW/",
"accession": "IGVFFI5182ZRIW",
"aliases": [
"jesse-engreitz:230523pPPIFEnformer-THP1-Amp_PPIF_promoter-BioRep1-FFrep1-FACS_Input-PCRrep2_R2"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2023-12-13T09:25:45.114712+00:00",
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"file_size": 12047764,
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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-BioRep1-FFRep1_BinAll-PCRrep2_S386_R2_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI4701UFRL/",
"accession": "IGVFFI4701UFRL",
"aliases": [
"jesse-engreitz:230523pPPIFEnformer-THP1-Amp_PPIF_promoter-BioRep1-FFrep1-FACS_Input-PCRrep2_I2"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2023-12-13T16:05:19.987525+00:00",
"file_format": "fastq",
"file_size": 2168520,
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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-BioRep1-FFRep1_BinAll-PCRrep2_S386_I2_001.fastq.gz",
"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": "2023-12-20T23:07:55.307679+00:00",
"samples": [
{
"@id": "/in-vitro-systems/IGVFSM0390WQRT/",
"@type": [
"InVitroSystem",
"Biosample",
"Sample",
"Item"
],
"accession": "IGVFSM0390WQRT",
"aliases": [
"jesse-engreitz:230523pPPIFEnformer-THP1-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_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": "2023-12-13T08:17:09.400088+00:00",
"summary": "unsorted FACS input CRISPR prime editing Variant-EFFECTS integrating a guide (sgRNA) library targeting sequence variants in a genomic locus",
"uuid": "987ed580-9483-4a2e-ab91-ee30d3d9bb92"
}