{
"@context": "/terms/",
"@id": "/measurement-sets/IGVFDS3176NEHG/",
"@type": [
"MeasurementSet",
"FileSet",
"Item"
],
"accession": "IGVFDS3176NEHG",
"aliases": [
"jesse-engreitz:220829_8merInsertion-Jurkat_NoStimulation-Amp_PPIF_promoter-BioRep3-FFrep2-BinE_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 [IGVFDS3176NEHG](/measurement-sets/IGVFDS3176NEHG/) has sequence file(s) [IGVFFI1578HVFD](/sequence-files/IGVFFI1578HVFD/), [IGVFFI4723LXRU](/sequence-files/IGVFFI4723LXRU/), [IGVFFI3885BJBR](/sequence-files/IGVFFI3885BJBR/), [IGVFFI5928RKHA](/sequence-files/IGVFFI5928RKHA/), [IGVFFI6819FULN](/sequence-files/IGVFFI6819FULN/), [IGVFFI1292MBVL](/sequence-files/IGVFFI1292MBVL/), [IGVFFI9577FNJQ](/sequence-files/IGVFFI9577FNJQ/), [IGVFFI6014XMXZ](/sequence-files/IGVFFI6014XMXZ/) 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/IGVFDS3176NEHG/"
},
{
"category": "missing sequence specification",
"detail": "Measurement set [IGVFDS3176NEHG](/measurement-sets/IGVFDS3176NEHG/) has sequence file(s): [IGVFFI1578HVFD](/sequence-files/IGVFFI1578HVFD/), [IGVFFI4723LXRU](/sequence-files/IGVFFI4723LXRU/), [IGVFFI3885BJBR](/sequence-files/IGVFFI3885BJBR/), [IGVFFI5928RKHA](/sequence-files/IGVFFI5928RKHA/), [IGVFFI6819FULN](/sequence-files/IGVFFI6819FULN/), [IGVFFI1292MBVL](/sequence-files/IGVFFI1292MBVL/), [IGVFFI9577FNJQ](/sequence-files/IGVFFI9577FNJQ/), [IGVFFI6014XMXZ](/sequence-files/IGVFFI6014XMXZ/) 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/IGVFDS3176NEHG/"
},
{
"category": "mismatched status",
"detail": "Released in vitro system [IGVFSM2353FEES](/in-vitro-systems/IGVFSM2353FEES/) 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/IGVFSM2353FEES/"
}
],
"WARNING": [
{
"category": "missing auxiliary set",
"detail": "Measurement set [IGVFDS3176NEHG](/measurement-sets/IGVFDS3176NEHG/) 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/IGVFDS3176NEHG/"
}
]
},
"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": "2023-11-30T22:47:43.294990+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/IGVFFI1578HVFD/",
"accession": "IGVFFI1578HVFD",
"aliases": [
"jesse-engreitz:220829_8merInsertion-Jurkat_NoStimulation-Amp_PPIF_promoter-BioRep3-FFrep2-BinE-PCRrep1_R1"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2023-12-05T18:45:36.731145+00:00",
"file_format": "fastq",
"file_size": 7414518,
"href": "/sequence-files/IGVFFI1578HVFD/@@download/IGVFFI1578HVFD.fastq.gz",
"s3_uri": "s3://igvf-files/2023/12/05/a1e953e7-9967-4497-8b9f-687c98cd1112/IGVFFI1578HVFD.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_S8-BioRep3-FFRep2-BinE-PCRrep1_S40_R1_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI4723LXRU/",
"accession": "IGVFFI4723LXRU",
"aliases": [
"jesse-engreitz:220829_8merInsertion-Jurkat_NoStimulation-Amp_PPIF_promoter-BioRep3-FFrep2-BinE-PCRrep2_I2"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2023-12-05T19:30:09.471723+00:00",
"file_format": "fastq",
"file_size": 2757717,
"href": "/sequence-files/IGVFFI4723LXRU/@@download/IGVFFI4723LXRU.fastq.gz",
"s3_uri": "s3://igvf-files/2023/12/05/fcb76f0a-5b4c-442c-8f12-d2fa465b853f/IGVFFI4723LXRU.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_S8-BioRep3-FFRep2-BinE-PCRrep2_S96_I2_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI3885BJBR/",
"accession": "IGVFFI3885BJBR",
"aliases": [
"jesse-engreitz:220829_8merInsertion-Jurkat_NoStimulation-Amp_PPIF_promoter-BioRep3-FFrep2-BinE-PCRrep1_I2"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2023-12-05T19:23:54.326391+00:00",
"file_format": "fastq",
"file_size": 3059345,
"href": "/sequence-files/IGVFFI3885BJBR/@@download/IGVFFI3885BJBR.fastq.gz",
"s3_uri": "s3://igvf-files/2023/12/05/66e69141-fe19-4db1-abed-2f4b2a527b38/IGVFFI3885BJBR.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_S8-BioRep3-FFRep2-BinE-PCRrep1_S40_I2_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI5928RKHA/",
"accession": "IGVFFI5928RKHA",
"aliases": [
"jesse-engreitz:220829_8merInsertion-Jurkat_NoStimulation-Amp_PPIF_promoter-BioRep3-FFrep2-BinE-PCRrep2_R2"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2023-12-05T19:05:03.718460+00:00",
"file_format": "fastq",
"file_size": 12036729,
"href": "/sequence-files/IGVFFI5928RKHA/@@download/IGVFFI5928RKHA.fastq.gz",
"s3_uri": "s3://igvf-files/2023/12/05/7172ea43-90e2-405a-bf0e-eaf543bbdf82/IGVFFI5928RKHA.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_S8-BioRep3-FFRep2-BinE-PCRrep2_S96_R2_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI6819FULN/",
"accession": "IGVFFI6819FULN",
"aliases": [
"jesse-engreitz:220829_8merInsertion-Jurkat_NoStimulation-Amp_PPIF_promoter-BioRep3-FFrep2-BinE-PCRrep2_R1"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2023-12-05T18:51:54.573494+00:00",
"file_format": "fastq",
"file_size": 6561480,
"href": "/sequence-files/IGVFFI6819FULN/@@download/IGVFFI6819FULN.fastq.gz",
"s3_uri": "s3://igvf-files/2023/12/05/c514ccc5-7da0-4676-8f6c-8d250b25e0e5/IGVFFI6819FULN.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_S8-BioRep3-FFRep2-BinE-PCRrep2_S96_R1_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI1292MBVL/",
"accession": "IGVFFI1292MBVL",
"aliases": [
"jesse-engreitz:220829_8merInsertion-Jurkat_NoStimulation-Amp_PPIF_promoter-BioRep3-FFrep2-BinE-PCRrep1_I1"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2023-12-05T19:11:18.597067+00:00",
"file_format": "fastq",
"file_size": 3092253,
"href": "/sequence-files/IGVFFI1292MBVL/@@download/IGVFFI1292MBVL.fastq.gz",
"s3_uri": "s3://igvf-files/2023/12/05/d83ce039-c007-4841-9974-680740a3b3f3/IGVFFI1292MBVL.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_S8-BioRep3-FFRep2-BinE-PCRrep1_S40_I1_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI9577FNJQ/",
"accession": "IGVFFI9577FNJQ",
"aliases": [
"jesse-engreitz:220829_8merInsertion-Jurkat_NoStimulation-Amp_PPIF_promoter-BioRep3-FFrep2-BinE-PCRrep2_I1"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2023-12-05T19:17:34.042758+00:00",
"file_format": "fastq",
"file_size": 2858911,
"href": "/sequence-files/IGVFFI9577FNJQ/@@download/IGVFFI9577FNJQ.fastq.gz",
"s3_uri": "s3://igvf-files/2023/12/05/0ac3dad2-e167-46c4-8fcd-2cad6d5b1b67/IGVFFI9577FNJQ.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_S8-BioRep3-FFRep2-BinE-PCRrep2_S96_I1_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI6014XMXZ/",
"accession": "IGVFFI6014XMXZ",
"aliases": [
"jesse-engreitz:220829_8merInsertion-Jurkat_NoStimulation-Amp_PPIF_promoter-BioRep3-FFrep2-BinE-PCRrep1_R2"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2023-12-05T18:58:26.057882+00:00",
"file_format": "fastq",
"file_size": 13563722,
"href": "/sequence-files/IGVFFI6014XMXZ/@@download/IGVFFI6014XMXZ.fastq.gz",
"s3_uri": "s3://igvf-files/2023/12/05/d5ec0ba3-50bc-47b2-8ff5-6e30453ff583/IGVFFI6014XMXZ.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_S8-BioRep3-FFRep2-BinE-PCRrep1_S40_R2_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": "2023-12-20T23:04:09.538291+00:00",
"samples": [
{
"@id": "/in-vitro-systems/IGVFSM2353FEES/",
"@type": [
"InVitroSystem",
"Biosample",
"Sample",
"Item"
],
"accession": "IGVFSM2353FEES",
"aliases": [
"jesse-engreitz:220829_8merInsertion-Jurkat_NoStimulation-Amp_PPIF_promoter-BioRep3-FFrep2-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": "2023-12-05T18:45:36.731145+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": "e583628a-dc44-4157-82ac-a8774f553f12"
}