{
"@context": "/terms/",
"@id": "/measurement-sets/IGVFDS7024RXFA/",
"@type": [
"MeasurementSet",
"FileSet",
"Item"
],
"accession": "IGVFDS7024RXFA",
"aliases": [
"jesse-engreitz:240426S024-PPIFenhancervalidation-THP1_Amp_PPIF_enhancer-BioRep2-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 [IGVFDS7024RXFA](/measurement-sets/IGVFDS7024RXFA/) has sequence file(s) [IGVFFI2400TQJA](/sequence-files/IGVFFI2400TQJA/), [IGVFFI4320FLGE](/sequence-files/IGVFFI4320FLGE/), [IGVFFI9495EOET](/sequence-files/IGVFFI9495EOET/), [IGVFFI7117XVVN](/sequence-files/IGVFFI7117XVVN/), [IGVFFI5832HUGJ](/sequence-files/IGVFFI5832HUGJ/), [IGVFFI4183UTPP](/sequence-files/IGVFFI4183UTPP/), [IGVFFI8254XUFD](/sequence-files/IGVFFI8254XUFD/), [IGVFFI5277NQDZ](/sequence-files/IGVFFI5277NQDZ/) 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/IGVFDS7024RXFA/"
},
{
"category": "missing sequence specification",
"detail": "Measurement set [IGVFDS7024RXFA](/measurement-sets/IGVFDS7024RXFA/) has sequence file(s): [IGVFFI2400TQJA](/sequence-files/IGVFFI2400TQJA/), [IGVFFI4320FLGE](/sequence-files/IGVFFI4320FLGE/), [IGVFFI9495EOET](/sequence-files/IGVFFI9495EOET/), [IGVFFI7117XVVN](/sequence-files/IGVFFI7117XVVN/), [IGVFFI5832HUGJ](/sequence-files/IGVFFI5832HUGJ/), [IGVFFI4183UTPP](/sequence-files/IGVFFI4183UTPP/), [IGVFFI8254XUFD](/sequence-files/IGVFFI8254XUFD/), [IGVFFI5277NQDZ](/sequence-files/IGVFFI5277NQDZ/) 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/IGVFDS7024RXFA/"
}
],
"WARNING": [
{
"category": "missing auxiliary set",
"detail": "Measurement set [IGVFDS7024RXFA](/measurement-sets/IGVFDS7024RXFA/) 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/IGVFDS7024RXFA/"
}
]
},
"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": "2024-11-25T23:54:03.263620+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/IGVFFI2400TQJA/",
"accession": "IGVFFI2400TQJA",
"aliases": [
"jesse-engreitz:240426S024-PPIFenhancervalidation-THP1_Amp_PPIF_enhancer-BioRep2-FFrep2-FACS_Input-PCRrep2_R1"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2024-11-26T07:28:19.430091+00:00",
"file_format": "fastq",
"file_size": 10048288,
"href": "/sequence-files/IGVFFI2400TQJA/@@download/IGVFFI2400TQJA.fastq.gz",
"s3_uri": "s3://igvf-files/2024/11/26/6f21729f-194c-496a-a033-ea5246e8b7ca/IGVFFI2400TQJA.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-FFrep2-BinAll-PCRrep2_S813_R1_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI4320FLGE/",
"accession": "IGVFFI4320FLGE",
"aliases": [
"jesse-engreitz:240426S024-PPIFenhancervalidation-THP1_Amp_PPIF_enhancer-BioRep2-FFrep2-FACS_Input-PCRrep1_R1"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2024-11-26T07:26:39.890341+00:00",
"file_format": "fastq",
"file_size": 10337413,
"href": "/sequence-files/IGVFFI4320FLGE/@@download/IGVFFI4320FLGE.fastq.gz",
"s3_uri": "s3://igvf-files/2024/11/26/01ead957-81f2-45a3-8988-c4479d9f8a47/IGVFFI4320FLGE.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-FFrep2-BinAll-PCRrep1_S804_R1_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI9495EOET/",
"accession": "IGVFFI9495EOET",
"aliases": [
"jesse-engreitz:240426S024-PPIFenhancervalidation-THP1_Amp_PPIF_enhancer-BioRep2-FFrep2-FACS_Input-PCRrep1_R2"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2024-11-26T10:22:23.570134+00:00",
"file_format": "fastq",
"file_size": 11938228,
"href": "/sequence-files/IGVFFI9495EOET/@@download/IGVFFI9495EOET.fastq.gz",
"s3_uri": "s3://igvf-files/2024/11/26/1632fc44-5035-4c5d-8246-2f8f2bcffcc0/IGVFFI9495EOET.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-FFrep2-BinAll-PCRrep1_S804_R2_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI7117XVVN/",
"accession": "IGVFFI7117XVVN",
"aliases": [
"jesse-engreitz:240426S024-PPIFenhancervalidation-THP1_Amp_PPIF_enhancer-BioRep2-FFrep2-FACS_Input-PCRrep2_R2"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2024-11-26T10:25:18.916261+00:00",
"file_format": "fastq",
"file_size": 11887547,
"href": "/sequence-files/IGVFFI7117XVVN/@@download/IGVFFI7117XVVN.fastq.gz",
"s3_uri": "s3://igvf-files/2024/11/26/3e5dac1e-2119-430f-9b90-224491761556/IGVFFI7117XVVN.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-FFrep2-BinAll-PCRrep2_S813_R2_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI5832HUGJ/",
"accession": "IGVFFI5832HUGJ",
"aliases": [
"jesse-engreitz:240426S024-PPIFenhancervalidation-THP1_Amp_PPIF_enhancer-BioRep2-FFrep2-FACS_Input-PCRrep1_I1"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2024-11-26T14:15:41.017560+00:00",
"file_format": "fastq",
"file_size": 4560677,
"href": "/sequence-files/IGVFFI5832HUGJ/@@download/IGVFFI5832HUGJ.fastq.gz",
"s3_uri": "s3://igvf-files/2024/11/26/4b5d583c-acc2-4f64-9cab-4477a5bd5b86/IGVFFI5832HUGJ.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-FFrep2-BinAll-PCRrep1_S804_I1_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI4183UTPP/",
"accession": "IGVFFI4183UTPP",
"aliases": [
"jesse-engreitz:240426S024-PPIFenhancervalidation-THP1_Amp_PPIF_enhancer-BioRep2-FFrep2-FACS_Input-PCRrep2_I1"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2024-11-26T14:18:27.532099+00:00",
"file_format": "fastq",
"file_size": 4423865,
"href": "/sequence-files/IGVFFI4183UTPP/@@download/IGVFFI4183UTPP.fastq.gz",
"s3_uri": "s3://igvf-files/2024/11/26/fe4f3435-61cc-44c1-827a-787d68786dbe/IGVFFI4183UTPP.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-FFrep2-BinAll-PCRrep2_S813_I1_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI8254XUFD/",
"accession": "IGVFFI8254XUFD",
"aliases": [
"jesse-engreitz:240426S024-PPIFenhancervalidation-THP1_Amp_PPIF_enhancer-BioRep2-FFrep2-FACS_Input-PCRrep1_I2"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2024-11-26T18:14:17.365811+00:00",
"file_format": "fastq",
"file_size": 4378963,
"href": "/sequence-files/IGVFFI8254XUFD/@@download/IGVFFI8254XUFD.fastq.gz",
"s3_uri": "s3://igvf-files/2024/11/26/5e5d4714-2694-4b56-9993-5e8cfcba8de1/IGVFFI8254XUFD.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-FFrep2-BinAll-PCRrep1_S804_I2_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI5277NQDZ/",
"accession": "IGVFFI5277NQDZ",
"aliases": [
"jesse-engreitz:240426S024-PPIFenhancervalidation-THP1_Amp_PPIF_enhancer-BioRep2-FFrep2-FACS_Input-PCRrep2_I2"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2024-11-26T18:17:05.389018+00:00",
"file_format": "fastq",
"file_size": 4347590,
"href": "/sequence-files/IGVFFI5277NQDZ/@@download/IGVFFI5277NQDZ.fastq.gz",
"s3_uri": "s3://igvf-files/2024/11/26/0de679ff-9188-4673-b1d8-ed89ebf3c801/IGVFFI5277NQDZ.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-FFrep2-BinAll-PCRrep2_S813_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/IGVFSM9480RXDI/",
"@type": [
"InVitroSystem",
"Biosample",
"Sample",
"Item"
],
"accession": "IGVFSM9480RXDI",
"aliases": [
"jesse-engreitz:240426S024-PPIFenhancervalidation-THP1_Amp_PPIF_enhancer-BioRep2-FFrep2-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": "2024-11-26T07:26:39.890341+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": "5d038a80-0efd-435a-99d5-0681d613874f"
}