{
"@context": "/terms/",
"@id": "/measurement-sets/IGVFDS7859TASD/",
"@type": [
"MeasurementSet",
"FileSet",
"Item"
],
"accession": "IGVFDS7859TASD",
"aliases": [
"jesse-engreitz:240908-S029-PPIF_5SpliceSite-IndividualVariantExp-AGGT_TCCA-THP1-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 [IGVFDS7859TASD](/measurement-sets/IGVFDS7859TASD/) has sequence file(s) [IGVFFI1619FDED](/sequence-files/IGVFFI1619FDED/), [IGVFFI4290XIZD](/sequence-files/IGVFFI4290XIZD/), [IGVFFI8923SAQP](/sequence-files/IGVFFI8923SAQP/), [IGVFFI2836ZXQS](/sequence-files/IGVFFI2836ZXQS/), [IGVFFI1713BHRU](/sequence-files/IGVFFI1713BHRU/), [IGVFFI2168LTUH](/sequence-files/IGVFFI2168LTUH/), [IGVFFI4650XMXL](/sequence-files/IGVFFI4650XMXL/), [IGVFFI6301PNSH](/sequence-files/IGVFFI6301PNSH/) 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/IGVFDS7859TASD/"
},
{
"category": "missing sequence specification",
"detail": "Measurement set [IGVFDS7859TASD](/measurement-sets/IGVFDS7859TASD/) has sequence file(s): [IGVFFI1619FDED](/sequence-files/IGVFFI1619FDED/), [IGVFFI4290XIZD](/sequence-files/IGVFFI4290XIZD/), [IGVFFI8923SAQP](/sequence-files/IGVFFI8923SAQP/), [IGVFFI2836ZXQS](/sequence-files/IGVFFI2836ZXQS/), [IGVFFI1713BHRU](/sequence-files/IGVFFI1713BHRU/), [IGVFFI2168LTUH](/sequence-files/IGVFFI2168LTUH/), [IGVFFI4650XMXL](/sequence-files/IGVFFI4650XMXL/), [IGVFFI6301PNSH](/sequence-files/IGVFFI6301PNSH/) 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/IGVFDS7859TASD/"
}
],
"WARNING": [
{
"category": "missing auxiliary set",
"detail": "Measurement set [IGVFDS7859TASD](/measurement-sets/IGVFDS7859TASD/) 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/IGVFDS7859TASD/"
}
]
},
"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/IGVFDS8210FQOO/",
"accession": "IGVFDS8210FQOO",
"aliases": [
"jesse-engreitz:THP1-PE2_Exp7_PPIF_5SpliceSite-IndividualVariantExp_NegControl_AmpliconSequencing"
],
"status": "preview"
}
],
"control_for": [],
"creation_timestamp": "2024-12-10T22:37:31.480142+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/IGVFFI1619FDED/",
"accession": "IGVFFI1619FDED",
"aliases": [
"jesse-engreitz:240908-S029-PPIF_5SpliceSite-IndividualVariantExp-AGGT_TCCA-THP1-BioRep1-FFrep1-FACS_Input-PCRrep1_R1"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2024-12-10T23:49:05.545963+00:00",
"file_format": "fastq",
"file_size": 34820644,
"href": "/sequence-files/IGVFFI1619FDED/@@download/IGVFFI1619FDED.fastq.gz",
"s3_uri": "s3://igvf-files/2024/12/10/1ac65dc1-bf53-49cd-bdd7-87ed3046964e/IGVFFI1619FDED.fastq.gz",
"sequencing_platform": {
"@id": "/platform-terms/EFO_0022840/",
"status": "released",
"term_name": "Illumina NovaSeq X"
},
"status": "preview",
"submitted_file_name": "240908-S029-5splice-THP1-5splicesite_C10-Amp_PPIF_5splicesite-BioRep1-FFrep1-BinAll-PCRrep1_S967_R1_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI4290XIZD/",
"accession": "IGVFFI4290XIZD",
"aliases": [
"jesse-engreitz:240908-S029-PPIF_5SpliceSite-IndividualVariantExp-AGGT_TCCA-THP1-BioRep1-FFrep1-FACS_Input-PCRrep2_R1"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2024-12-10T23:52:05.567094+00:00",
"file_format": "fastq",
"file_size": 38575289,
"href": "/sequence-files/IGVFFI4290XIZD/@@download/IGVFFI4290XIZD.fastq.gz",
"s3_uri": "s3://igvf-files/2024/12/10/b2b59b4c-56eb-4f94-a3d7-4dc47a96ef4e/IGVFFI4290XIZD.fastq.gz",
"sequencing_platform": {
"@id": "/platform-terms/EFO_0022840/",
"status": "released",
"term_name": "Illumina NovaSeq X"
},
"status": "preview",
"submitted_file_name": "240908-S029-5splice-THP1-5splicesite_C10-Amp_PPIF_5splicesite-BioRep1-FFrep1-BinAll-PCRrep2_S979_R1_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI8923SAQP/",
"accession": "IGVFFI8923SAQP",
"aliases": [
"jesse-engreitz:240908-S029-PPIF_5SpliceSite-IndividualVariantExp-AGGT_TCCA-THP1-BioRep1-FFrep1-FACS_Input-PCRrep2_R2"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2024-12-11T16:57:32.089196+00:00",
"file_format": "fastq",
"file_size": 33158019,
"href": "/sequence-files/IGVFFI8923SAQP/@@download/IGVFFI8923SAQP.fastq.gz",
"s3_uri": "s3://igvf-files/2024/12/11/2a6418ae-d70a-4d7a-ac0f-d6d72d9fae09/IGVFFI8923SAQP.fastq.gz",
"sequencing_platform": {
"@id": "/platform-terms/EFO_0022840/",
"status": "released",
"term_name": "Illumina NovaSeq X"
},
"status": "preview",
"submitted_file_name": "240908-S029-5splice-THP1-5splicesite_C10-Amp_PPIF_5splicesite-BioRep1-FFrep1-BinAll-PCRrep2_S979_R2_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI2836ZXQS/",
"accession": "IGVFFI2836ZXQS",
"aliases": [
"jesse-engreitz:240908-S029-PPIF_5SpliceSite-IndividualVariantExp-AGGT_TCCA-THP1-BioRep1-FFrep1-FACS_Input-PCRrep1_R2"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2024-12-11T16:56:02.096509+00:00",
"file_format": "fastq",
"file_size": 29966551,
"href": "/sequence-files/IGVFFI2836ZXQS/@@download/IGVFFI2836ZXQS.fastq.gz",
"s3_uri": "s3://igvf-files/2024/12/11/9620da2a-d15d-4bbc-b6e4-6fc2cabe3ede/IGVFFI2836ZXQS.fastq.gz",
"sequencing_platform": {
"@id": "/platform-terms/EFO_0022840/",
"status": "released",
"term_name": "Illumina NovaSeq X"
},
"status": "preview",
"submitted_file_name": "240908-S029-5splice-THP1-5splicesite_C10-Amp_PPIF_5splicesite-BioRep1-FFrep1-BinAll-PCRrep1_S967_R2_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI1713BHRU/",
"accession": "IGVFFI1713BHRU",
"aliases": [
"jesse-engreitz:240908-S029-PPIF_5SpliceSite-IndividualVariantExp-AGGT_TCCA-THP1-BioRep1-FFrep1-FACS_Input-PCRrep2_I1"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2024-12-11T20:33:38.802316+00:00",
"file_format": "fastq",
"file_size": 13517256,
"href": "/sequence-files/IGVFFI1713BHRU/@@download/IGVFFI1713BHRU.fastq.gz",
"s3_uri": "s3://igvf-files/2024/12/11/91d39c16-9012-4807-8bb4-8fcb83109bba/IGVFFI1713BHRU.fastq.gz",
"sequencing_platform": {
"@id": "/platform-terms/EFO_0022840/",
"status": "released",
"term_name": "Illumina NovaSeq X"
},
"status": "preview",
"submitted_file_name": "240908-S029-5splice-THP1-5splicesite_C10-Amp_PPIF_5splicesite-BioRep1-FFrep1-BinAll-PCRrep2_S979_I1_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI2168LTUH/",
"accession": "IGVFFI2168LTUH",
"aliases": [
"jesse-engreitz:240908-S029-PPIF_5SpliceSite-IndividualVariantExp-AGGT_TCCA-THP1-BioRep1-FFrep1-FACS_Input-PCRrep1_I1"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2024-12-11T20:30:44.884510+00:00",
"file_format": "fastq",
"file_size": 11983735,
"href": "/sequence-files/IGVFFI2168LTUH/@@download/IGVFFI2168LTUH.fastq.gz",
"s3_uri": "s3://igvf-files/2024/12/11/198e2932-42c7-486b-9f8c-cd6cf81ea667/IGVFFI2168LTUH.fastq.gz",
"sequencing_platform": {
"@id": "/platform-terms/EFO_0022840/",
"status": "released",
"term_name": "Illumina NovaSeq X"
},
"status": "preview",
"submitted_file_name": "240908-S029-5splice-THP1-5splicesite_C10-Amp_PPIF_5splicesite-BioRep1-FFrep1-BinAll-PCRrep1_S967_I1_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI4650XMXL/",
"accession": "IGVFFI4650XMXL",
"aliases": [
"jesse-engreitz:240908-S029-PPIF_5SpliceSite-IndividualVariantExp-AGGT_TCCA-THP1-BioRep1-FFrep1-FACS_Input-PCRrep2_I2"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2024-12-11T22:46:17.194947+00:00",
"file_format": "fastq",
"file_size": 12730371,
"href": "/sequence-files/IGVFFI4650XMXL/@@download/IGVFFI4650XMXL.fastq.gz",
"s3_uri": "s3://igvf-files/2024/12/11/54d3b289-8eae-48e3-b1a6-b6541d938ed2/IGVFFI4650XMXL.fastq.gz",
"sequencing_platform": {
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"status": "released",
"term_name": "Illumina NovaSeq X"
},
"status": "preview",
"submitted_file_name": "240908-S029-5splice-THP1-5splicesite_C10-Amp_PPIF_5splicesite-BioRep1-FFrep1-BinAll-PCRrep2_S979_I2_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI6301PNSH/",
"accession": "IGVFFI6301PNSH",
"aliases": [
"jesse-engreitz:240908-S029-PPIF_5SpliceSite-IndividualVariantExp-AGGT_TCCA-THP1-BioRep1-FFrep1-FACS_Input-PCRrep1_I2"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2024-12-11T22:43:15.692169+00:00",
"file_format": "fastq",
"file_size": 11310049,
"href": "/sequence-files/IGVFFI6301PNSH/@@download/IGVFFI6301PNSH.fastq.gz",
"s3_uri": "s3://igvf-files/2024/12/11/7e9bb9ec-39f8-4ff1-a0e3-376fa3815622/IGVFFI6301PNSH.fastq.gz",
"sequencing_platform": {
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"status": "released",
"term_name": "Illumina NovaSeq X"
},
"status": "preview",
"submitted_file_name": "240908-S029-5splice-THP1-5splicesite_C10-Amp_PPIF_5splicesite-BioRep1-FFrep1-BinAll-PCRrep1_S967_I2_001.fastq.gz",
"upload_status": "validated"
}
],
"input_for": [
"/analysis-sets/IGVFDS8267JJHO/"
],
"lab": {
"@id": "/labs/jesse-engreitz/",
"title": "Jesse Engreitz, Stanford"
},
"preferred_assay_title": "Variant-EFFECTS",
"protocols": [
"https://www.protocols.io/view/flowfish-with-primeflow-36wgq3q4olk5/v1"
],
"samples": [
{
"@id": "/in-vitro-systems/IGVFSM2894EXAV/",
"@type": [
"InVitroSystem",
"Biosample",
"Sample",
"Item"
],
"accession": "IGVFSM2894EXAV",
"aliases": [
"jesse-engreitz:240908-S029-PPIF_5SpliceSite-IndividualVariantExp-AGGT_TCCA-THP1-BioRep1-FFrep1-FACS_Input"
],
"classifications": [
"cell line"
],
"construct_library_sets": [
{
"@id": "/construct-library-sets/IGVFDS9097TEUZ/",
"accession": "IGVFDS9097TEUZ",
"file_set_type": "guide library",
"status": "preview",
"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": "preview",
"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": "preview",
"submitted_by": {
"@id": "/users/f9e7cd82-a407-4a20-89ee-f4dc668b0cbe/",
"title": "Michael Montgomery"
},
"submitted_files_timestamp": "2024-12-10T23:49:05.545963+00:00",
"summary": "CRISPR prime editing Variant-EFFECTS integrating a guide (sgRNA) library targeting sequence variants in a genomic locus",
"targeted_genes": [
{
"@id": "/genes/ENSG00000108179/",
"geneid": "ENSG00000108179",
"name": "peptidylprolyl isomerase F",
"status": "released",
"symbol": "PPIF",
"synonyms": [
"rotamase F",
"CYP3",
"cyclophilin F",
"mitochondrial cyclophilin",
"peptidyl-prolyl cis-trans isomerase, mitochondrial",
"CypD",
"Cyp-D",
"cyclophilin 3",
"cyclophilin D",
"CyP-M",
"peptidyl-prolyl cis-trans isomerase F, mitochondrial",
"PPIase F"
]
}
],
"uuid": "34365588-066c-4d4e-9bef-9ca60f52cf1e"
}