{
"@context": "/terms/",
"@id": "/measurement-sets/IGVFDS8639XKMS/",
"@type": [
"MeasurementSet",
"FileSet",
"Item"
],
"accession": "IGVFDS8639XKMS",
"aliases": [
"jesse-engreitz:220829_8merInsertion-Jurkat_NoStimulation-Amp_PPIF_promoter-BioRep2-FFrep2-BinF_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 [IGVFDS8639XKMS](/measurement-sets/IGVFDS8639XKMS/) has sequence file(s) [IGVFFI4143LEQS](/sequence-files/IGVFFI4143LEQS/), [IGVFFI1193DZTF](/sequence-files/IGVFFI1193DZTF/), [IGVFFI2716QPFU](/sequence-files/IGVFFI2716QPFU/), [IGVFFI8448AXTU](/sequence-files/IGVFFI8448AXTU/), [IGVFFI9829QTRV](/sequence-files/IGVFFI9829QTRV/), [IGVFFI8815RUPC](/sequence-files/IGVFFI8815RUPC/), [IGVFFI5509DEGW](/sequence-files/IGVFFI5509DEGW/), [IGVFFI6759AWNV](/sequence-files/IGVFFI6759AWNV/) 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/IGVFDS8639XKMS/"
},
{
"category": "missing sequence specification",
"detail": "Measurement set [IGVFDS8639XKMS](/measurement-sets/IGVFDS8639XKMS/) has sequence file(s): [IGVFFI4143LEQS](/sequence-files/IGVFFI4143LEQS/), [IGVFFI1193DZTF](/sequence-files/IGVFFI1193DZTF/), [IGVFFI2716QPFU](/sequence-files/IGVFFI2716QPFU/), [IGVFFI8448AXTU](/sequence-files/IGVFFI8448AXTU/), [IGVFFI9829QTRV](/sequence-files/IGVFFI9829QTRV/), [IGVFFI8815RUPC](/sequence-files/IGVFFI8815RUPC/), [IGVFFI5509DEGW](/sequence-files/IGVFFI5509DEGW/), [IGVFFI6759AWNV](/sequence-files/IGVFFI6759AWNV/) 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/IGVFDS8639XKMS/"
},
{
"category": "mismatched status",
"detail": "Released in vitro system [IGVFSM9304LUZX](/in-vitro-systems/IGVFSM9304LUZX/) 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/IGVFSM9304LUZX/"
}
],
"WARNING": [
{
"category": "missing auxiliary set",
"detail": "Measurement set [IGVFDS8639XKMS](/measurement-sets/IGVFDS8639XKMS/) 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/IGVFDS8639XKMS/"
}
]
},
"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": "2023-11-30T22:47:29.273360+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/IGVFFI4143LEQS/",
"accession": "IGVFFI4143LEQS",
"aliases": [
"jesse-engreitz:220829_8merInsertion-Jurkat_NoStimulation-Amp_PPIF_promoter-BioRep2-FFrep2-BinF-PCRrep2_I2"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2023-12-05T19:28:16.101762+00:00",
"file_format": "fastq",
"file_size": 3212781,
"href": "/sequence-files/IGVFFI4143LEQS/@@download/IGVFFI4143LEQS.fastq.gz",
"s3_uri": "s3://igvf-files/2023/12/05/4f4adcf6-a74a-4f65-a416-76afd20832fe/IGVFFI4143LEQS.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_S6-BioRep2-FFRep2-BinF-PCRrep2_S83_I2_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI1193DZTF/",
"accession": "IGVFFI1193DZTF",
"aliases": [
"jesse-engreitz:220829_8merInsertion-Jurkat_NoStimulation-Amp_PPIF_promoter-BioRep2-FFrep2-BinF-PCRrep2_I1"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2023-12-05T19:15:40.546340+00:00",
"file_format": "fastq",
"file_size": 3390981,
"href": "/sequence-files/IGVFFI1193DZTF/@@download/IGVFFI1193DZTF.fastq.gz",
"s3_uri": "s3://igvf-files/2023/12/05/4f3ae2ee-ba88-46a2-b237-af64d905decc/IGVFFI1193DZTF.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_S6-BioRep2-FFRep2-BinF-PCRrep2_S83_I1_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI2716QPFU/",
"accession": "IGVFFI2716QPFU",
"aliases": [
"jesse-engreitz:220829_8merInsertion-Jurkat_NoStimulation-Amp_PPIF_promoter-BioRep2-FFrep2-BinF-PCRrep2_R1"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2023-12-05T18:50:00.553139+00:00",
"file_format": "fastq",
"file_size": 7819883,
"href": "/sequence-files/IGVFFI2716QPFU/@@download/IGVFFI2716QPFU.fastq.gz",
"s3_uri": "s3://igvf-files/2023/12/05/a8bb430e-ac06-49d7-8d57-f726d9171cee/IGVFFI2716QPFU.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_S6-BioRep2-FFRep2-BinF-PCRrep2_S83_R1_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI8448AXTU/",
"accession": "IGVFFI8448AXTU",
"aliases": [
"jesse-engreitz:220829_8merInsertion-Jurkat_NoStimulation-Amp_PPIF_promoter-BioRep2-FFrep2-BinF-PCRrep1_R1"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2023-12-05T18:43:41.530592+00:00",
"file_format": "fastq",
"file_size": 7844002,
"href": "/sequence-files/IGVFFI8448AXTU/@@download/IGVFFI8448AXTU.fastq.gz",
"s3_uri": "s3://igvf-files/2023/12/05/ab8bc772-c26f-4ca0-b935-1b4e8417c741/IGVFFI8448AXTU.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_S6-BioRep2-FFRep2-BinF-PCRrep1_S27_R1_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI9829QTRV/",
"accession": "IGVFFI9829QTRV",
"aliases": [
"jesse-engreitz:220829_8merInsertion-Jurkat_NoStimulation-Amp_PPIF_promoter-BioRep2-FFrep2-BinF-PCRrep1_I2"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2023-12-05T19:21:57.317443+00:00",
"file_format": "fastq",
"file_size": 3223894,
"href": "/sequence-files/IGVFFI9829QTRV/@@download/IGVFFI9829QTRV.fastq.gz",
"s3_uri": "s3://igvf-files/2023/12/05/1c6750b5-98e5-493d-855a-fbdcada0d4c4/IGVFFI9829QTRV.fastq.gz",
"sequencing_platform": {
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"status": "released",
"term_name": "Illumina NextSeq 550"
},
"status": "released",
"submitted_file_name": "220829_pPPIF_JurkatVFF-Jurkat-PE2A-BFP-pPPIF-Amp_pPPIF_S6-BioRep2-FFRep2-BinF-PCRrep1_S27_I2_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI8815RUPC/",
"accession": "IGVFFI8815RUPC",
"aliases": [
"jesse-engreitz:220829_8merInsertion-Jurkat_NoStimulation-Amp_PPIF_promoter-BioRep2-FFrep2-BinF-PCRrep2_R2"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2023-12-05T19:03:04.770862+00:00",
"file_format": "fastq",
"file_size": 14303743,
"href": "/sequence-files/IGVFFI8815RUPC/@@download/IGVFFI8815RUPC.fastq.gz",
"s3_uri": "s3://igvf-files/2023/12/05/0fbc22f6-d1c3-4b40-9600-0fd7a21f1790/IGVFFI8815RUPC.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_S6-BioRep2-FFRep2-BinF-PCRrep2_S83_R2_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI5509DEGW/",
"accession": "IGVFFI5509DEGW",
"aliases": [
"jesse-engreitz:220829_8merInsertion-Jurkat_NoStimulation-Amp_PPIF_promoter-BioRep2-FFrep2-BinF-PCRrep1_R2"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2023-12-05T18:56:27.499471+00:00",
"file_format": "fastq",
"file_size": 14293800,
"href": "/sequence-files/IGVFFI5509DEGW/@@download/IGVFFI5509DEGW.fastq.gz",
"s3_uri": "s3://igvf-files/2023/12/05/d8c4cf86-ea46-4d8c-84b4-efd4a996ec6e/IGVFFI5509DEGW.fastq.gz",
"sequencing_platform": {
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"status": "released",
"term_name": "Illumina NextSeq 550"
},
"status": "released",
"submitted_file_name": "220829_pPPIF_JurkatVFF-Jurkat-PE2A-BFP-pPPIF-Amp_pPPIF_S6-BioRep2-FFRep2-BinF-PCRrep1_S27_R2_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI6759AWNV/",
"accession": "IGVFFI6759AWNV",
"aliases": [
"jesse-engreitz:220829_8merInsertion-Jurkat_NoStimulation-Amp_PPIF_promoter-BioRep2-FFrep2-BinF-PCRrep1_I1"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2023-12-05T19:09:25.133581+00:00",
"file_format": "fastq",
"file_size": 3319498,
"href": "/sequence-files/IGVFFI6759AWNV/@@download/IGVFFI6759AWNV.fastq.gz",
"s3_uri": "s3://igvf-files/2023/12/05/6790b01b-b352-407b-955e-b40a7fd31e1f/IGVFFI6759AWNV.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_S6-BioRep2-FFRep2-BinF-PCRrep1_S27_I1_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": "2023-12-20T23:09:41.940911+00:00",
"samples": [
{
"@id": "/in-vitro-systems/IGVFSM9304LUZX/",
"@type": [
"InVitroSystem",
"Biosample",
"Sample",
"Item"
],
"accession": "IGVFSM9304LUZX",
"aliases": [
"jesse-engreitz:220829_8merInsertion-Jurkat_NoStimulation-Amp_PPIF_promoter-BioRep2-FFrep2-BinF"
],
"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 90-100% 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": "2023-12-05T18:43:41.530592+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": "29194f3f-4ae4-46eb-a29d-5dd818ef2daf"
}