{
"@context": "/terms/",
"@id": "/measurement-sets/IGVFDS7603YHCC/",
"@type": [
"MeasurementSet",
"FileSet",
"Item"
],
"accession": "IGVFDS7603YHCC",
"aliases": [
"jesse-engreitz:220829_8merInsertion-Jurkat_NoStimulation-Amp_PPIF_promoter-BioRep1-FFrep2-BinD_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 [IGVFSM4545VFSU](/in-vitro-systems/IGVFSM4545VFSU/) has in progress subobject construct library set [IGVFDS6377KNCH](/construct-library-sets/IGVFDS6377KNCH/).",
"level": 30,
"level_name": "INTERNAL_ACTION",
"name": "audit_item_status",
"path": "/in-vitro-systems/IGVFSM4545VFSU/"
},
{
"category": "missing sequencing kit",
"detail": "Measurement set [IGVFDS7603YHCC](/measurement-sets/IGVFDS7603YHCC/) has sequence file(s) [IGVFFI9034LPIS](/sequence-files/IGVFFI9034LPIS/), [IGVFFI3678XPSO](/sequence-files/IGVFFI3678XPSO/), [IGVFFI4723QNLP](/sequence-files/IGVFFI4723QNLP/), [IGVFFI1153MKLD](/sequence-files/IGVFFI1153MKLD/), [IGVFFI2537PIQZ](/sequence-files/IGVFFI2537PIQZ/), [IGVFFI0460SDWQ](/sequence-files/IGVFFI0460SDWQ/), [IGVFFI0936QWIF](/sequence-files/IGVFFI0936QWIF/), [IGVFFI4896GLOW](/sequence-files/IGVFFI4896GLOW/) 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/IGVFDS7603YHCC/"
},
{
"category": "missing sequence specification",
"detail": "Measurement set [IGVFDS7603YHCC](/measurement-sets/IGVFDS7603YHCC/) has sequence file(s): [IGVFFI9034LPIS](/sequence-files/IGVFFI9034LPIS/), [IGVFFI3678XPSO](/sequence-files/IGVFFI3678XPSO/), [IGVFFI4723QNLP](/sequence-files/IGVFFI4723QNLP/), [IGVFFI1153MKLD](/sequence-files/IGVFFI1153MKLD/), [IGVFFI2537PIQZ](/sequence-files/IGVFFI2537PIQZ/), [IGVFFI0460SDWQ](/sequence-files/IGVFFI0460SDWQ/), [IGVFFI0936QWIF](/sequence-files/IGVFFI0936QWIF/), [IGVFFI4896GLOW](/sequence-files/IGVFFI4896GLOW/) 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/IGVFDS7603YHCC/"
}
],
"WARNING": [
{
"category": "missing auxiliary set",
"detail": "Measurement set [IGVFDS7603YHCC](/measurement-sets/IGVFDS7603YHCC/) 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/IGVFDS7603YHCC/"
}
]
},
"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/IGVFDS9477ARWI/",
"accession": "IGVFDS9477ARWI",
"aliases": [
"jesse-engreitz:220829_8merInsertion-Jurkat_NoStimulation-Amp_PPIF_promoter-Jurkat-PE2_Exp1_NegControl_AmpliconSequencing",
"jesse-engreitz:220829_8merInsertion-Jurkat_Stimulation-Amp_PPIF_promoter-Jurkat-PE2_Exp1_NegControl_AmpliconSequencing"
],
"status": "released"
}
],
"control_for": [],
"creation_timestamp": "2023-11-30T22:47:12.150353+00:00",
"donors": [
{
"@id": "/human-donors/IGVFDO1080XFGV/",
"accession": "IGVFDO1080XFGV",
"aliases": [
"igvf:donor_of_Jurkat"
],
"sex": "male",
"status": "released",
"taxa": "Homo sapiens"
}
],
"externally_hosted": false,
"file_set_type": "experimental data",
"files": [
{
"@id": "/sequence-files/IGVFFI9034LPIS/",
"accession": "IGVFFI9034LPIS",
"aliases": [
"jesse-engreitz:220829_8merInsertion-Jurkat_NoStimulation-Amp_PPIF_promoter-BioRep1-FFrep2-BinD-PCRrep1_I2"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2023-12-05T19:19:36.316494+00:00",
"file_format": "fastq",
"file_size": 3204534,
"href": "/sequence-files/IGVFFI9034LPIS/@@download/IGVFFI9034LPIS.fastq.gz",
"s3_uri": "s3://igvf-files/2023/12/05/61c2a2fb-4f4b-4c3c-80d9-bcd042cc8b77/IGVFFI9034LPIS.fastq.gz",
"sequencing_platform": {
"@id": "/platform-terms/EFO_0008566/",
"status": "released",
"term_name": "Illumina NextSeq 550"
},
"status": "released",
"submitted_file_name": "220829_pPPIF_JurkatVFF-Jurkat-PE2A-BFP-pPPIF-Amp_pPPIF_S3-BioRep1-FFRep2-BinD-PCRrep1_S11_I2_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI3678XPSO/",
"accession": "IGVFFI3678XPSO",
"aliases": [
"jesse-engreitz:220829_8merInsertion-Jurkat_NoStimulation-Amp_PPIF_promoter-BioRep1-FFrep2-BinD-PCRrep2_R1"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2023-12-05T18:47:39.734138+00:00",
"file_format": "fastq",
"file_size": 7746652,
"href": "/sequence-files/IGVFFI3678XPSO/@@download/IGVFFI3678XPSO.fastq.gz",
"s3_uri": "s3://igvf-files/2023/12/05/0537a462-ec8f-4d47-ac26-f5644a152322/IGVFFI3678XPSO.fastq.gz",
"sequencing_platform": {
"@id": "/platform-terms/EFO_0008566/",
"status": "released",
"term_name": "Illumina NextSeq 550"
},
"status": "released",
"submitted_file_name": "220829_pPPIF_JurkatVFF-Jurkat-PE2A-BFP-pPPIF-Amp_pPPIF_S3-BioRep1-FFRep2-BinD-PCRrep2_S67_R1_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI4723QNLP/",
"accession": "IGVFFI4723QNLP",
"aliases": [
"jesse-engreitz:220829_8merInsertion-Jurkat_NoStimulation-Amp_PPIF_promoter-BioRep1-FFrep2-BinD-PCRrep2_I1"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2023-12-05T19:13:20.981279+00:00",
"file_format": "fastq",
"file_size": 3350263,
"href": "/sequence-files/IGVFFI4723QNLP/@@download/IGVFFI4723QNLP.fastq.gz",
"s3_uri": "s3://igvf-files/2023/12/05/f80c72ac-6c2f-470a-9a75-e6f7d83778b4/IGVFFI4723QNLP.fastq.gz",
"sequencing_platform": {
"@id": "/platform-terms/EFO_0008566/",
"status": "released",
"term_name": "Illumina NextSeq 550"
},
"status": "released",
"submitted_file_name": "220829_pPPIF_JurkatVFF-Jurkat-PE2A-BFP-pPPIF-Amp_pPPIF_S3-BioRep1-FFRep2-BinD-PCRrep2_S67_I1_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI1153MKLD/",
"accession": "IGVFFI1153MKLD",
"aliases": [
"jesse-engreitz:220829_8merInsertion-Jurkat_NoStimulation-Amp_PPIF_promoter-BioRep1-FFrep2-BinD-PCRrep1_I1"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2023-12-05T19:07:07.060146+00:00",
"file_format": "fastq",
"file_size": 3365351,
"href": "/sequence-files/IGVFFI1153MKLD/@@download/IGVFFI1153MKLD.fastq.gz",
"s3_uri": "s3://igvf-files/2023/12/05/99eddfc3-811f-4a4b-8247-d2ab09d5c9a9/IGVFFI1153MKLD.fastq.gz",
"sequencing_platform": {
"@id": "/platform-terms/EFO_0008566/",
"status": "released",
"term_name": "Illumina NextSeq 550"
},
"status": "released",
"submitted_file_name": "220829_pPPIF_JurkatVFF-Jurkat-PE2A-BFP-pPPIF-Amp_pPPIF_S3-BioRep1-FFRep2-BinD-PCRrep1_S11_I1_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI2537PIQZ/",
"accession": "IGVFFI2537PIQZ",
"aliases": [
"jesse-engreitz:220829_8merInsertion-Jurkat_NoStimulation-Amp_PPIF_promoter-BioRep1-FFrep2-BinD-PCRrep1_R2"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2023-12-05T18:54:02.056068+00:00",
"file_format": "fastq",
"file_size": 14244598,
"href": "/sequence-files/IGVFFI2537PIQZ/@@download/IGVFFI2537PIQZ.fastq.gz",
"s3_uri": "s3://igvf-files/2023/12/05/28195c28-6db7-45fc-b435-200b98af8209/IGVFFI2537PIQZ.fastq.gz",
"sequencing_platform": {
"@id": "/platform-terms/EFO_0008566/",
"status": "released",
"term_name": "Illumina NextSeq 550"
},
"status": "released",
"submitted_file_name": "220829_pPPIF_JurkatVFF-Jurkat-PE2A-BFP-pPPIF-Amp_pPPIF_S3-BioRep1-FFRep2-BinD-PCRrep1_S11_R2_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI0460SDWQ/",
"accession": "IGVFFI0460SDWQ",
"aliases": [
"jesse-engreitz:220829_8merInsertion-Jurkat_NoStimulation-Amp_PPIF_promoter-BioRep1-FFrep2-BinD-PCRrep2_R2"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2023-12-05T19:00:37.581805+00:00",
"file_format": "fastq",
"file_size": 14247196,
"href": "/sequence-files/IGVFFI0460SDWQ/@@download/IGVFFI0460SDWQ.fastq.gz",
"s3_uri": "s3://igvf-files/2023/12/05/b3e5bec5-6826-455f-b9bd-62947bd7f8f5/IGVFFI0460SDWQ.fastq.gz",
"sequencing_platform": {
"@id": "/platform-terms/EFO_0008566/",
"status": "released",
"term_name": "Illumina NextSeq 550"
},
"status": "released",
"submitted_file_name": "220829_pPPIF_JurkatVFF-Jurkat-PE2A-BFP-pPPIF-Amp_pPPIF_S3-BioRep1-FFRep2-BinD-PCRrep2_S67_R2_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI0936QWIF/",
"accession": "IGVFFI0936QWIF",
"aliases": [
"jesse-engreitz:220829_8merInsertion-Jurkat_NoStimulation-Amp_PPIF_promoter-BioRep1-FFrep2-BinD-PCRrep2_I2"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2023-12-05T19:25:57.210842+00:00",
"file_format": "fastq",
"file_size": 3187591,
"href": "/sequence-files/IGVFFI0936QWIF/@@download/IGVFFI0936QWIF.fastq.gz",
"s3_uri": "s3://igvf-files/2023/12/05/ea765052-34b6-4f9f-8490-465aa3cc82d1/IGVFFI0936QWIF.fastq.gz",
"sequencing_platform": {
"@id": "/platform-terms/EFO_0008566/",
"status": "released",
"term_name": "Illumina NextSeq 550"
},
"status": "released",
"submitted_file_name": "220829_pPPIF_JurkatVFF-Jurkat-PE2A-BFP-pPPIF-Amp_pPPIF_S3-BioRep1-FFRep2-BinD-PCRrep2_S67_I2_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI4896GLOW/",
"accession": "IGVFFI4896GLOW",
"aliases": [
"jesse-engreitz:220829_8merInsertion-Jurkat_NoStimulation-Amp_PPIF_promoter-BioRep1-FFrep2-BinD-PCRrep1_R1"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2023-12-05T18:41:21.375751+00:00",
"file_format": "fastq",
"file_size": 7809567,
"href": "/sequence-files/IGVFFI4896GLOW/@@download/IGVFFI4896GLOW.fastq.gz",
"s3_uri": "s3://igvf-files/2023/12/05/1e2be9f7-46a0-422b-85a7-06dd67ba4212/IGVFFI4896GLOW.fastq.gz",
"sequencing_platform": {
"@id": "/platform-terms/EFO_0008566/",
"status": "released",
"term_name": "Illumina NextSeq 550"
},
"status": "released",
"submitted_file_name": "220829_pPPIF_JurkatVFF-Jurkat-PE2A-BFP-pPPIF-Amp_pPPIF_S3-BioRep1-FFRep2-BinD-PCRrep1_S11_R1_001.fastq.gz",
"upload_status": "validated"
}
],
"input_for": [
"/analysis-sets/IGVFDS9162RHFP/"
],
"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": "2023-12-20T23:04:12.099270+00:00",
"samples": [
{
"@id": "/in-vitro-systems/IGVFSM4545VFSU/",
"@type": [
"InVitroSystem",
"Biosample",
"Sample",
"Item"
],
"accession": "IGVFSM4545VFSU",
"aliases": [
"jesse-engreitz:220829_8merInsertion-Jurkat_NoStimulation-Amp_PPIF_promoter-BioRep1-FFrep2-BinD"
],
"classifications": [
"cell line"
],
"construct_library_sets": [
{
"@id": "/construct-library-sets/IGVFDS6377KNCH/",
"accession": "IGVFDS6377KNCH",
"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_0002796/",
"@type": [
"SampleTerm",
"OntologyTerm",
"Item"
],
"aliases": [
"igvf:Jurkat"
],
"status": "released",
"summary": "Jurkat",
"term_name": "Jurkat"
}
],
"status": "released",
"summary": "Jurkat cell line, male, Homo sapiens (sorting details: FACS bin for 55-65% expression of PPIF) 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": "2023-12-05T18:41:21.375751+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": "54fd1150-ddc3-4384-9bd4-177d3f24717a"
}