{
"@context": "/terms/",
"@id": "/measurement-sets/IGVFDS4188FAAP/",
"@type": [
"MeasurementSet",
"FileSet",
"Item"
],
"accession": "IGVFDS4188FAAP",
"aliases": [
"jesse-engreitz:230523pPPIFEnformer-THP1-Amp_PPIF_promoter-BioRep1-FFrep4-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 [IGVFSM2170CHPM](/in-vitro-systems/IGVFSM2170CHPM/) 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/IGVFSM2170CHPM/"
},
{
"category": "missing sequencing kit",
"detail": "Measurement set [IGVFDS4188FAAP](/measurement-sets/IGVFDS4188FAAP/) has sequence file(s) [IGVFFI6116CTIO](/sequence-files/IGVFFI6116CTIO/), [IGVFFI0893HCNA](/sequence-files/IGVFFI0893HCNA/), [IGVFFI5146MIXM](/sequence-files/IGVFFI5146MIXM/), [IGVFFI8554ZNZM](/sequence-files/IGVFFI8554ZNZM/), [IGVFFI5211IPLK](/sequence-files/IGVFFI5211IPLK/), [IGVFFI7441VGDL](/sequence-files/IGVFFI7441VGDL/), [IGVFFI6314ZRDC](/sequence-files/IGVFFI6314ZRDC/), [IGVFFI0729VBPU](/sequence-files/IGVFFI0729VBPU/) 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/IGVFDS4188FAAP/"
},
{
"category": "missing sequence specification",
"detail": "Measurement set [IGVFDS4188FAAP](/measurement-sets/IGVFDS4188FAAP/) has sequence file(s): [IGVFFI6116CTIO](/sequence-files/IGVFFI6116CTIO/), [IGVFFI0893HCNA](/sequence-files/IGVFFI0893HCNA/), [IGVFFI5146MIXM](/sequence-files/IGVFFI5146MIXM/), [IGVFFI8554ZNZM](/sequence-files/IGVFFI8554ZNZM/), [IGVFFI5211IPLK](/sequence-files/IGVFFI5211IPLK/), [IGVFFI7441VGDL](/sequence-files/IGVFFI7441VGDL/), [IGVFFI6314ZRDC](/sequence-files/IGVFFI6314ZRDC/), [IGVFFI0729VBPU](/sequence-files/IGVFFI0729VBPU/) 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/IGVFDS4188FAAP/"
}
],
"WARNING": [
{
"category": "missing auxiliary set",
"detail": "Measurement set [IGVFDS4188FAAP](/measurement-sets/IGVFDS4188FAAP/) 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/IGVFDS4188FAAP/"
},
{
"category": "missing targeted genes",
"detail": "Measurement set [IGVFDS4188FAAP](/measurement-sets/IGVFDS4188FAAP/) 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/IGVFDS4188FAAP/"
}
]
},
"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": "2023-12-13T08:01:42.960577+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": [
{
"@id": "/sequence-files/IGVFFI6116CTIO/",
"accession": "IGVFFI6116CTIO",
"aliases": [
"jesse-engreitz:230523pPPIFEnformer-THP1-Amp_PPIF_promoter-BioRep1-FFrep4-FACS_Input-PCRrep1_I2"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2023-12-13T16:28:31.722917+00:00",
"file_format": "fastq",
"file_size": 2113768,
"href": "/sequence-files/IGVFFI6116CTIO/@@download/IGVFFI6116CTIO.fastq.gz",
"s3_uri": "s3://igvf-files/2023/12/13/3c8dea12-9fff-47a2-b3b1-fe0ce3c11b0a/IGVFFI6116CTIO.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-FFRep4_BinAll-PCRrep1_S391_I2_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI0893HCNA/",
"accession": "IGVFFI0893HCNA",
"aliases": [
"jesse-engreitz:230523pPPIFEnformer-THP1-Amp_PPIF_promoter-BioRep1-FFrep4-FACS_Input-PCRrep2_R2"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2023-12-13T09:51:26.435745+00:00",
"file_format": "fastq",
"file_size": 11918053,
"href": "/sequence-files/IGVFFI0893HCNA/@@download/IGVFFI0893HCNA.fastq.gz",
"s3_uri": "s3://igvf-files/2023/12/13/5e5e293f-d42f-424f-b4b4-b759911e6e97/IGVFFI0893HCNA.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-FFRep4_BinAll-PCRrep2_S392_R2_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI5146MIXM/",
"accession": "IGVFFI5146MIXM",
"aliases": [
"jesse-engreitz:230523pPPIFEnformer-THP1-Amp_PPIF_promoter-BioRep1-FFrep4-FACS_Input-PCRrep2_R1"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2023-12-13T08:43:30.319796+00:00",
"file_format": "fastq",
"file_size": 9492412,
"href": "/sequence-files/IGVFFI5146MIXM/@@download/IGVFFI5146MIXM.fastq.gz",
"s3_uri": "s3://igvf-files/2023/12/13/9abebbd3-227c-49d1-b550-4ae4e0388fc9/IGVFFI5146MIXM.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-FFRep4_BinAll-PCRrep2_S392_R1_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI8554ZNZM/",
"accession": "IGVFFI8554ZNZM",
"aliases": [
"jesse-engreitz:230523pPPIFEnformer-THP1-Amp_PPIF_promoter-BioRep1-FFrep4-FACS_Input-PCRrep2_I1"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2023-12-13T15:25:35.559383+00:00",
"file_format": "fastq",
"file_size": 2287211,
"href": "/sequence-files/IGVFFI8554ZNZM/@@download/IGVFFI8554ZNZM.fastq.gz",
"s3_uri": "s3://igvf-files/2023/12/13/580e7591-fa75-41f1-b692-133ed862b2b0/IGVFFI8554ZNZM.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-FFRep4_BinAll-PCRrep2_S392_I1_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI5211IPLK/",
"accession": "IGVFFI5211IPLK",
"aliases": [
"jesse-engreitz:230523pPPIFEnformer-THP1-Amp_PPIF_promoter-BioRep1-FFrep4-FACS_Input-PCRrep1_I1"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2023-12-13T15:24:48.377824+00:00",
"file_format": "fastq",
"file_size": 2228579,
"href": "/sequence-files/IGVFFI5211IPLK/@@download/IGVFFI5211IPLK.fastq.gz",
"s3_uri": "s3://igvf-files/2023/12/13/4048d562-4308-460d-89bc-ebfe80cd49a0/IGVFFI5211IPLK.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-FFRep4_BinAll-PCRrep1_S391_I1_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI7441VGDL/",
"accession": "IGVFFI7441VGDL",
"aliases": [
"jesse-engreitz:230523pPPIFEnformer-THP1-Amp_PPIF_promoter-BioRep1-FFrep4-FACS_Input-PCRrep1_R1"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2023-12-13T08:42:40.000009+00:00",
"file_format": "fastq",
"file_size": 9534082,
"href": "/sequence-files/IGVFFI7441VGDL/@@download/IGVFFI7441VGDL.fastq.gz",
"s3_uri": "s3://igvf-files/2023/12/13/2dbdd1c4-d36c-4fc5-b708-782a3cd67f01/IGVFFI7441VGDL.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-FFRep4_BinAll-PCRrep1_S391_R1_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI6314ZRDC/",
"accession": "IGVFFI6314ZRDC",
"aliases": [
"jesse-engreitz:230523pPPIFEnformer-THP1-Amp_PPIF_promoter-BioRep1-FFrep4-FACS_Input-PCRrep2_I2"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2023-12-13T16:29:19.260308+00:00",
"file_format": "fastq",
"file_size": 2133300,
"href": "/sequence-files/IGVFFI6314ZRDC/@@download/IGVFFI6314ZRDC.fastq.gz",
"s3_uri": "s3://igvf-files/2023/12/13/1a9791ee-7259-4615-9e0f-a3511d117ca2/IGVFFI6314ZRDC.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-FFRep4_BinAll-PCRrep2_S392_I2_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI0729VBPU/",
"accession": "IGVFFI0729VBPU",
"aliases": [
"jesse-engreitz:230523pPPIFEnformer-THP1-Amp_PPIF_promoter-BioRep1-FFrep4-FACS_Input-PCRrep1_R2"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2023-12-13T09:50:36.878541+00:00",
"file_format": "fastq",
"file_size": 11994624,
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"s3_uri": "s3://igvf-files/2023/12/13/55fa248d-992c-4f4f-a851-5d45187488ab/IGVFFI0729VBPU.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-FFRep4_BinAll-PCRrep1_S391_R2_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": "2023-12-20T23:07:49.695132+00:00",
"samples": [
{
"@id": "/in-vitro-systems/IGVFSM2170CHPM/",
"@type": [
"InVitroSystem",
"Biosample",
"Sample",
"Item"
],
"accession": "IGVFSM2170CHPM",
"aliases": [
"jesse-engreitz:230523pPPIFEnformer-THP1-Amp_PPIF_promoter-BioRep1-FFrep4-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": "2023-12-13T08:42:40.000009+00:00",
"summary": "unsorted FACS input CRISPR prime editing Variant-EFFECTS integrating a guide (sgRNA) library targeting sequence variants in a genomic locus",
"uuid": "98882200-b667-4b42-8e1e-cda951f87b60"
}