{
"@context": "/terms/",
"@id": "/measurement-sets/IGVFDS3397KUUP/",
"@type": [
"MeasurementSet",
"FileSet",
"Item"
],
"accession": "IGVFDS3397KUUP",
"aliases": [
"jesse-engreitz:240426S024-PPIFenhancervalidation-THP1_Amp_PPIF_enhancer-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 [IGVFDS3397KUUP](/measurement-sets/IGVFDS3397KUUP/) has sequence file(s) [IGVFFI5282IAVX](/sequence-files/IGVFFI5282IAVX/), [IGVFFI9618QTJG](/sequence-files/IGVFFI9618QTJG/), [IGVFFI3396UWKI](/sequence-files/IGVFFI3396UWKI/), [IGVFFI3473FBNJ](/sequence-files/IGVFFI3473FBNJ/), [IGVFFI4607MOSQ](/sequence-files/IGVFFI4607MOSQ/), [IGVFFI7957JVBT](/sequence-files/IGVFFI7957JVBT/), [IGVFFI0942MOOD](/sequence-files/IGVFFI0942MOOD/), [IGVFFI8765ZNWL](/sequence-files/IGVFFI8765ZNWL/) 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/IGVFDS3397KUUP/"
},
{
"category": "missing sequence specification",
"detail": "Measurement set [IGVFDS3397KUUP](/measurement-sets/IGVFDS3397KUUP/) has sequence file(s): [IGVFFI5282IAVX](/sequence-files/IGVFFI5282IAVX/), [IGVFFI9618QTJG](/sequence-files/IGVFFI9618QTJG/), [IGVFFI3396UWKI](/sequence-files/IGVFFI3396UWKI/), [IGVFFI3473FBNJ](/sequence-files/IGVFFI3473FBNJ/), [IGVFFI4607MOSQ](/sequence-files/IGVFFI4607MOSQ/), [IGVFFI7957JVBT](/sequence-files/IGVFFI7957JVBT/), [IGVFFI0942MOOD](/sequence-files/IGVFFI0942MOOD/), [IGVFFI8765ZNWL](/sequence-files/IGVFFI8765ZNWL/) 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/IGVFDS3397KUUP/"
}
],
"WARNING": [
{
"category": "missing auxiliary set",
"detail": "Measurement set [IGVFDS3397KUUP](/measurement-sets/IGVFDS3397KUUP/) 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/IGVFDS3397KUUP/"
}
]
},
"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/IGVFDS4103BJLT/",
"accession": "IGVFDS4103BJLT",
"aliases": [
"jesse-engreitz:240426S024-PPIFenhancervalidation-THP1_Amp_PPIF_enhancer-THP1-PE2_Exp4_NegControl_AmpliconSequencing"
],
"status": "preview"
}
],
"control_for": [],
"creation_timestamp": "2024-11-25T23:54:25.457546+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": "IGVFFI5282IAVX",
"aliases": [
"jesse-engreitz:240426S024-PPIFenhancervalidation-THP1_Amp_PPIF_enhancer-BioRep2-FFrep3-FACS_Input-PCRrep1_R1"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2024-11-26T07:42:09.231426+00:00",
"file_format": "fastq",
"file_size": 9203872,
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"sequencing_platform": {
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"status": "released",
"term_name": "Illumina NovaSeq X"
},
"status": "preview",
"submitted_file_name": "240426S024-Enhancer-THP1-PPIF_Enhancer_val_guides-Amp_PPIF_enhancer-BioRep2-FFrep3-BinAll-PCRrep1_S805_R1_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI9618QTJG/",
"accession": "IGVFFI9618QTJG",
"aliases": [
"jesse-engreitz:240426S024-PPIFenhancervalidation-THP1_Amp_PPIF_enhancer-BioRep2-FFrep3-FACS_Input-PCRrep2_R1"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2024-11-26T07:43:36.519588+00:00",
"file_format": "fastq",
"file_size": 10042252,
"href": "/sequence-files/IGVFFI9618QTJG/@@download/IGVFFI9618QTJG.fastq.gz",
"s3_uri": "s3://igvf-files/2024/11/26/cc055a0e-f849-4d34-b61d-aff2e4a802ed/IGVFFI9618QTJG.fastq.gz",
"sequencing_platform": {
"@id": "/platform-terms/EFO_0022840/",
"status": "released",
"term_name": "Illumina NovaSeq X"
},
"status": "preview",
"submitted_file_name": "240426S024-Enhancer-THP1-PPIF_Enhancer_val_guides-Amp_PPIF_enhancer-BioRep2-FFrep3-BinAll-PCRrep2_S814_R1_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI3396UWKI/",
"accession": "IGVFFI3396UWKI",
"aliases": [
"jesse-engreitz:240426S024-PPIFenhancervalidation-THP1_Amp_PPIF_enhancer-BioRep2-FFrep3-FACS_Input-PCRrep2_R2"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2024-11-26T10:54:07.014462+00:00",
"file_format": "fastq",
"file_size": 11764313,
"href": "/sequence-files/IGVFFI3396UWKI/@@download/IGVFFI3396UWKI.fastq.gz",
"s3_uri": "s3://igvf-files/2024/11/26/b0733734-56c0-4e1d-a2f3-5e1216aa0139/IGVFFI3396UWKI.fastq.gz",
"sequencing_platform": {
"@id": "/platform-terms/EFO_0022840/",
"status": "released",
"term_name": "Illumina NovaSeq X"
},
"status": "preview",
"submitted_file_name": "240426S024-Enhancer-THP1-PPIF_Enhancer_val_guides-Amp_PPIF_enhancer-BioRep2-FFrep3-BinAll-PCRrep2_S814_R2_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI3473FBNJ/",
"accession": "IGVFFI3473FBNJ",
"aliases": [
"jesse-engreitz:240426S024-PPIFenhancervalidation-THP1_Amp_PPIF_enhancer-BioRep2-FFrep3-FACS_Input-PCRrep1_R2"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2024-11-26T10:51:15.282919+00:00",
"file_format": "fastq",
"file_size": 10815630,
"href": "/sequence-files/IGVFFI3473FBNJ/@@download/IGVFFI3473FBNJ.fastq.gz",
"s3_uri": "s3://igvf-files/2024/11/26/83944b3f-3978-4b5f-ab75-72443b7470d9/IGVFFI3473FBNJ.fastq.gz",
"sequencing_platform": {
"@id": "/platform-terms/EFO_0022840/",
"status": "released",
"term_name": "Illumina NovaSeq X"
},
"status": "preview",
"submitted_file_name": "240426S024-Enhancer-THP1-PPIF_Enhancer_val_guides-Amp_PPIF_enhancer-BioRep2-FFrep3-BinAll-PCRrep1_S805_R2_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI4607MOSQ/",
"accession": "IGVFFI4607MOSQ",
"aliases": [
"jesse-engreitz:240426S024-PPIFenhancervalidation-THP1_Amp_PPIF_enhancer-BioRep2-FFrep3-FACS_Input-PCRrep1_I1"
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"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2024-11-26T14:44:55.173785+00:00",
"file_format": "fastq",
"file_size": 4380323,
"href": "/sequence-files/IGVFFI4607MOSQ/@@download/IGVFFI4607MOSQ.fastq.gz",
"s3_uri": "s3://igvf-files/2024/11/26/feae52ec-cc26-4c28-a297-a0e431ba0f51/IGVFFI4607MOSQ.fastq.gz",
"sequencing_platform": {
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"status": "released",
"term_name": "Illumina NovaSeq X"
},
"status": "preview",
"submitted_file_name": "240426S024-Enhancer-THP1-PPIF_Enhancer_val_guides-Amp_PPIF_enhancer-BioRep2-FFrep3-BinAll-PCRrep1_S805_I1_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI7957JVBT/",
"accession": "IGVFFI7957JVBT",
"aliases": [
"jesse-engreitz:240426S024-PPIFenhancervalidation-THP1_Amp_PPIF_enhancer-BioRep2-FFrep3-FACS_Input-PCRrep2_I1"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2024-11-26T14:47:42.965701+00:00",
"file_format": "fastq",
"file_size": 4142620,
"href": "/sequence-files/IGVFFI7957JVBT/@@download/IGVFFI7957JVBT.fastq.gz",
"s3_uri": "s3://igvf-files/2024/11/26/4a9b4adc-8170-46e8-9dd4-d6dea8e18865/IGVFFI7957JVBT.fastq.gz",
"sequencing_platform": {
"@id": "/platform-terms/EFO_0022840/",
"status": "released",
"term_name": "Illumina NovaSeq X"
},
"status": "preview",
"submitted_file_name": "240426S024-Enhancer-THP1-PPIF_Enhancer_val_guides-Amp_PPIF_enhancer-BioRep2-FFrep3-BinAll-PCRrep2_S814_I1_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI0942MOOD/",
"accession": "IGVFFI0942MOOD",
"aliases": [
"jesse-engreitz:240426S024-PPIFenhancervalidation-THP1_Amp_PPIF_enhancer-BioRep2-FFrep3-FACS_Input-PCRrep2_I2"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2024-11-26T18:46:00.507869+00:00",
"file_format": "fastq",
"file_size": 4195313,
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"sequencing_platform": {
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"status": "released",
"term_name": "Illumina NovaSeq X"
},
"status": "preview",
"submitted_file_name": "240426S024-Enhancer-THP1-PPIF_Enhancer_val_guides-Amp_PPIF_enhancer-BioRep2-FFrep3-BinAll-PCRrep2_S814_I2_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI8765ZNWL/",
"accession": "IGVFFI8765ZNWL",
"aliases": [
"jesse-engreitz:240426S024-PPIFenhancervalidation-THP1_Amp_PPIF_enhancer-BioRep2-FFrep3-FACS_Input-PCRrep1_I2"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2024-11-26T18:43:02.679065+00:00",
"file_format": "fastq",
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"sequencing_platform": {
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"status": "released",
"term_name": "Illumina NovaSeq X"
},
"status": "preview",
"submitted_file_name": "240426S024-Enhancer-THP1-PPIF_Enhancer_val_guides-Amp_PPIF_enhancer-BioRep2-FFrep3-BinAll-PCRrep1_S805_I2_001.fastq.gz",
"upload_status": "validated"
}
],
"input_for": [
"/analysis-sets/IGVFDS4833ZRTZ/"
],
"lab": {
"@id": "/labs/jesse-engreitz/",
"title": "Jesse Engreitz, Stanford"
},
"notes": "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"
],
"samples": [
{
"@id": "/in-vitro-systems/IGVFSM0265ATLR/",
"@type": [
"InVitroSystem",
"Biosample",
"Sample",
"Item"
],
"accession": "IGVFSM0265ATLR",
"aliases": [
"jesse-engreitz:240426S024-PPIFenhancervalidation-THP1_Amp_PPIF_enhancer-BioRep2-FFrep3-FACS_Input"
],
"classifications": [
"cell line"
],
"construct_library_sets": [
{
"@id": "/construct-library-sets/IGVFDS4955GEYO/",
"accession": "IGVFDS4955GEYO",
"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": "2024-11-26T07:42:09.231426+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": "49aeb286-7c33-499b-b276-5d3de617f394"
}