{
"@context": "/terms/",
"@id": "/measurement-sets/IGVFDS9318EBEM/",
"@type": [
"MeasurementSet",
"FileSet",
"Item"
],
"accession": "IGVFDS9318EBEM",
"aliases": [
"jesse-engreitz:220829_8merInsertion-Jurkat_NoStimulation-Amp_PPIF_promoter-BioRep3-FFrep1-BinE_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 [IGVFSM8860VRBK](/in-vitro-systems/IGVFSM8860VRBK/) 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/IGVFSM8860VRBK/"
},
{
"category": "missing sequencing kit",
"detail": "Measurement set [IGVFDS9318EBEM](/measurement-sets/IGVFDS9318EBEM/) has sequence file(s) [IGVFFI6338WEEW](/sequence-files/IGVFFI6338WEEW/), [IGVFFI2927PWOX](/sequence-files/IGVFFI2927PWOX/), [IGVFFI9504SNHI](/sequence-files/IGVFFI9504SNHI/), [IGVFFI3230YLBU](/sequence-files/IGVFFI3230YLBU/), [IGVFFI6129FSTA](/sequence-files/IGVFFI6129FSTA/), [IGVFFI6767WEBU](/sequence-files/IGVFFI6767WEBU/), [IGVFFI5066GSPM](/sequence-files/IGVFFI5066GSPM/), [IGVFFI3259YVDH](/sequence-files/IGVFFI3259YVDH/) 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/IGVFDS9318EBEM/"
},
{
"category": "missing sequence specification",
"detail": "Measurement set [IGVFDS9318EBEM](/measurement-sets/IGVFDS9318EBEM/) has sequence file(s): [IGVFFI6338WEEW](/sequence-files/IGVFFI6338WEEW/), [IGVFFI2927PWOX](/sequence-files/IGVFFI2927PWOX/), [IGVFFI9504SNHI](/sequence-files/IGVFFI9504SNHI/), [IGVFFI3230YLBU](/sequence-files/IGVFFI3230YLBU/), [IGVFFI6129FSTA](/sequence-files/IGVFFI6129FSTA/), [IGVFFI6767WEBU](/sequence-files/IGVFFI6767WEBU/), [IGVFFI5066GSPM](/sequence-files/IGVFFI5066GSPM/), [IGVFFI3259YVDH](/sequence-files/IGVFFI3259YVDH/) 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/IGVFDS9318EBEM/"
}
],
"WARNING": [
{
"category": "missing auxiliary set",
"detail": "Measurement set [IGVFDS9318EBEM](/measurement-sets/IGVFDS9318EBEM/) 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/IGVFDS9318EBEM/"
}
]
},
"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": "2023-11-30T22:47:35.279881+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/IGVFFI6338WEEW/",
"accession": "IGVFFI6338WEEW",
"aliases": [
"jesse-engreitz:220829_8merInsertion-Jurkat_NoStimulation-Amp_PPIF_promoter-BioRep3-FFrep1-BinE-PCRrep2_R2"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2023-12-05T19:03:59.326696+00:00",
"file_format": "fastq",
"file_size": 13803420,
"href": "/sequence-files/IGVFFI6338WEEW/@@download/IGVFFI6338WEEW.fastq.gz",
"s3_uri": "s3://igvf-files/2023/12/05/06f9d107-bc7d-42d6-a0f6-b1af05541a13/IGVFFI6338WEEW.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_S7-BioRep3-FFRep1-BinE-PCRrep2_S89_R2_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI2927PWOX/",
"accession": "IGVFFI2927PWOX",
"aliases": [
"jesse-engreitz:220829_8merInsertion-Jurkat_NoStimulation-Amp_PPIF_promoter-BioRep3-FFrep1-BinE-PCRrep2_I1"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2023-12-05T19:16:32.997814+00:00",
"file_format": "fastq",
"file_size": 3354694,
"href": "/sequence-files/IGVFFI2927PWOX/@@download/IGVFFI2927PWOX.fastq.gz",
"s3_uri": "s3://igvf-files/2023/12/05/d81753ea-7cc6-4c25-9eae-a1beecec5706/IGVFFI2927PWOX.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_S7-BioRep3-FFRep1-BinE-PCRrep2_S89_I1_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI9504SNHI/",
"accession": "IGVFFI9504SNHI",
"aliases": [
"jesse-engreitz:220829_8merInsertion-Jurkat_NoStimulation-Amp_PPIF_promoter-BioRep3-FFrep1-BinE-PCRrep1_I2"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2023-12-05T19:22:49.873826+00:00",
"file_format": "fastq",
"file_size": 2958608,
"href": "/sequence-files/IGVFFI9504SNHI/@@download/IGVFFI9504SNHI.fastq.gz",
"s3_uri": "s3://igvf-files/2023/12/05/adf38792-159e-4c3d-bd64-2b57cfa5b891/IGVFFI9504SNHI.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_S7-BioRep3-FFRep1-BinE-PCRrep1_S33_I2_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI3230YLBU/",
"accession": "IGVFFI3230YLBU",
"aliases": [
"jesse-engreitz:220829_8merInsertion-Jurkat_NoStimulation-Amp_PPIF_promoter-BioRep3-FFrep1-BinE-PCRrep1_R1"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2023-12-05T18:44:34.017041+00:00",
"file_format": "fastq",
"file_size": 7189381,
"href": "/sequence-files/IGVFFI3230YLBU/@@download/IGVFFI3230YLBU.fastq.gz",
"s3_uri": "s3://igvf-files/2023/12/05/5360b113-6c21-4fba-af67-e39e4acc961b/IGVFFI3230YLBU.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_S7-BioRep3-FFRep1-BinE-PCRrep1_S33_R1_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI6129FSTA/",
"accession": "IGVFFI6129FSTA",
"aliases": [
"jesse-engreitz:220829_8merInsertion-Jurkat_NoStimulation-Amp_PPIF_promoter-BioRep3-FFrep1-BinE-PCRrep1_R2"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2023-12-05T18:57:22.337299+00:00",
"file_format": "fastq",
"file_size": 13120207,
"href": "/sequence-files/IGVFFI6129FSTA/@@download/IGVFFI6129FSTA.fastq.gz",
"s3_uri": "s3://igvf-files/2023/12/05/87240894-4624-425e-b720-b43e577c5ee1/IGVFFI6129FSTA.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_S7-BioRep3-FFRep1-BinE-PCRrep1_S33_R2_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI6767WEBU/",
"accession": "IGVFFI6767WEBU",
"aliases": [
"jesse-engreitz:220829_8merInsertion-Jurkat_NoStimulation-Amp_PPIF_promoter-BioRep3-FFrep1-BinE-PCRrep2_I2"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2023-12-05T19:29:08.239570+00:00",
"file_format": "fastq",
"file_size": 3113506,
"href": "/sequence-files/IGVFFI6767WEBU/@@download/IGVFFI6767WEBU.fastq.gz",
"s3_uri": "s3://igvf-files/2023/12/05/4847d579-4055-4d53-af18-5dd4ed41ec05/IGVFFI6767WEBU.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_S7-BioRep3-FFRep1-BinE-PCRrep2_S89_I2_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI5066GSPM/",
"accession": "IGVFFI5066GSPM",
"aliases": [
"jesse-engreitz:220829_8merInsertion-Jurkat_NoStimulation-Amp_PPIF_promoter-BioRep3-FFrep1-BinE-PCRrep1_I1"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2023-12-05T19:10:17.611837+00:00",
"file_format": "fastq",
"file_size": 3151891,
"href": "/sequence-files/IGVFFI5066GSPM/@@download/IGVFFI5066GSPM.fastq.gz",
"s3_uri": "s3://igvf-files/2023/12/05/075a1fc1-414b-4b4e-bcc6-f7c9ccbf9036/IGVFFI5066GSPM.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_S7-BioRep3-FFRep1-BinE-PCRrep1_S33_I1_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI3259YVDH/",
"accession": "IGVFFI3259YVDH",
"aliases": [
"jesse-engreitz:220829_8merInsertion-Jurkat_NoStimulation-Amp_PPIF_promoter-BioRep3-FFrep1-BinE-PCRrep2_R1"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2023-12-05T18:50:53.068020+00:00",
"file_format": "fastq",
"file_size": 7543313,
"href": "/sequence-files/IGVFFI3259YVDH/@@download/IGVFFI3259YVDH.fastq.gz",
"s3_uri": "s3://igvf-files/2023/12/05/3b949fa3-a368-4375-943a-81cbd9551905/IGVFFI3259YVDH.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_S7-BioRep3-FFRep1-BinE-PCRrep2_S89_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": "2023-12-20T23:04:45.861134+00:00",
"samples": [
{
"@id": "/in-vitro-systems/IGVFSM8860VRBK/",
"@type": [
"InVitroSystem",
"Biosample",
"Sample",
"Item"
],
"accession": "IGVFSM8860VRBK",
"aliases": [
"jesse-engreitz:220829_8merInsertion-Jurkat_NoStimulation-Amp_PPIF_promoter-BioRep3-FFrep1-BinE"
],
"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 80-90% 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": "2023-12-05T18:44:34.017041+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": "43e1373e-bac8-413b-9aad-a456f76ae498"
}