{
"@context": "/terms/",
"@id": "/measurement-sets/IGVFDS9915DQXW/",
"@type": [
"MeasurementSet",
"FileSet",
"Item"
],
"accession": "IGVFDS9915DQXW",
"aliases": [
"jesse-engreitz:220829_8merInsertion-Jurkat_NoStimulation-Amp_PPIF_promoter-BioRep1-FFrep1-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 [IGVFSM2723TUEN](/in-vitro-systems/IGVFSM2723TUEN/) 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/IGVFSM2723TUEN/"
},
{
"category": "missing sequencing kit",
"detail": "Measurement set [IGVFDS9915DQXW](/measurement-sets/IGVFDS9915DQXW/) has sequence file(s) [IGVFFI5706NIGC](/sequence-files/IGVFFI5706NIGC/), [IGVFFI5438IJFY](/sequence-files/IGVFFI5438IJFY/), [IGVFFI2919MRNA](/sequence-files/IGVFFI2919MRNA/), [IGVFFI6688MFBZ](/sequence-files/IGVFFI6688MFBZ/), [IGVFFI4195KVAX](/sequence-files/IGVFFI4195KVAX/), [IGVFFI9655VCDB](/sequence-files/IGVFFI9655VCDB/), [IGVFFI7610MRKW](/sequence-files/IGVFFI7610MRKW/), [IGVFFI5240CWOQ](/sequence-files/IGVFFI5240CWOQ/) 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/IGVFDS9915DQXW/"
},
{
"category": "missing sequence specification",
"detail": "Measurement set [IGVFDS9915DQXW](/measurement-sets/IGVFDS9915DQXW/) has sequence file(s): [IGVFFI5706NIGC](/sequence-files/IGVFFI5706NIGC/), [IGVFFI5438IJFY](/sequence-files/IGVFFI5438IJFY/), [IGVFFI2919MRNA](/sequence-files/IGVFFI2919MRNA/), [IGVFFI6688MFBZ](/sequence-files/IGVFFI6688MFBZ/), [IGVFFI4195KVAX](/sequence-files/IGVFFI4195KVAX/), [IGVFFI9655VCDB](/sequence-files/IGVFFI9655VCDB/), [IGVFFI7610MRKW](/sequence-files/IGVFFI7610MRKW/), [IGVFFI5240CWOQ](/sequence-files/IGVFFI5240CWOQ/) 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/IGVFDS9915DQXW/"
}
],
"WARNING": [
{
"category": "missing auxiliary set",
"detail": "Measurement set [IGVFDS9915DQXW](/measurement-sets/IGVFDS9915DQXW/) 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/IGVFDS9915DQXW/"
}
]
},
"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": "2023-12-01T00:02:55.107739+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/IGVFFI5706NIGC/",
"accession": "IGVFFI5706NIGC",
"aliases": [
"jesse-engreitz:220829_8merInsertion-Jurkat_NoStimulation-Amp_PPIF_promoter-BioRep1-FFrep1-BinD-PCRrep1_R2"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2023-12-05T18:52:57.690816+00:00",
"file_format": "fastq",
"file_size": 12337607,
"href": "/sequence-files/IGVFFI5706NIGC/@@download/IGVFFI5706NIGC.fastq.gz",
"s3_uri": "s3://igvf-files/2023/12/05/23977391-69b0-4aef-8a6b-81809e6ddcbf/IGVFFI5706NIGC.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_S2-BioRep1-FFRep1-BinD-PCRrep1_S4_R2_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI5438IJFY/",
"accession": "IGVFFI5438IJFY",
"aliases": [
"jesse-engreitz:220829_8merInsertion-Jurkat_NoStimulation-Amp_PPIF_promoter-BioRep1-FFrep1-BinD-PCRrep2_I1"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2023-12-05T19:12:19.698319+00:00",
"file_format": "fastq",
"file_size": 3307136,
"href": "/sequence-files/IGVFFI5438IJFY/@@download/IGVFFI5438IJFY.fastq.gz",
"s3_uri": "s3://igvf-files/2023/12/05/d4e570bb-19a2-40bf-a167-08a05794d51d/IGVFFI5438IJFY.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_S2-BioRep1-FFRep1-BinD-PCRrep2_S60_I1_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI2919MRNA/",
"accession": "IGVFFI2919MRNA",
"aliases": [
"jesse-engreitz:220829_8merInsertion-Jurkat_NoStimulation-Amp_PPIF_promoter-BioRep1-FFrep1-BinD-PCRrep2_R1"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2023-12-05T18:46:38.260633+00:00",
"file_format": "fastq",
"file_size": 7794211,
"href": "/sequence-files/IGVFFI2919MRNA/@@download/IGVFFI2919MRNA.fastq.gz",
"s3_uri": "s3://igvf-files/2023/12/05/fb3ba4c8-f96f-45d6-84b2-1d1435ee8922/IGVFFI2919MRNA.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_S2-BioRep1-FFRep1-BinD-PCRrep2_S60_R1_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI6688MFBZ/",
"accession": "IGVFFI6688MFBZ",
"aliases": [
"jesse-engreitz:220829_8merInsertion-Jurkat_NoStimulation-Amp_PPIF_promoter-BioRep1-FFrep1-BinD-PCRrep1_R1"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2023-12-05T18:40:18.857894+00:00",
"file_format": "fastq",
"file_size": 6735695,
"href": "/sequence-files/IGVFFI6688MFBZ/@@download/IGVFFI6688MFBZ.fastq.gz",
"s3_uri": "s3://igvf-files/2023/12/05/58e4ddca-a1ce-4e32-9500-806d6aef9eb5/IGVFFI6688MFBZ.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_S2-BioRep1-FFRep1-BinD-PCRrep1_S4_R1_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI4195KVAX/",
"accession": "IGVFFI4195KVAX",
"aliases": [
"jesse-engreitz:220829_8merInsertion-Jurkat_NoStimulation-Amp_PPIF_promoter-BioRep1-FFrep1-BinD-PCRrep2_R2"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2023-12-05T18:59:30.360693+00:00",
"file_format": "fastq",
"file_size": 14269144,
"href": "/sequence-files/IGVFFI4195KVAX/@@download/IGVFFI4195KVAX.fastq.gz",
"s3_uri": "s3://igvf-files/2023/12/05/6cd49396-b919-4a7f-b1b8-d8e02a5bd0f7/IGVFFI4195KVAX.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_S2-BioRep1-FFRep1-BinD-PCRrep2_S60_R2_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI9655VCDB/",
"accession": "IGVFFI9655VCDB",
"aliases": [
"jesse-engreitz:220829_8merInsertion-Jurkat_NoStimulation-Amp_PPIF_promoter-BioRep1-FFrep1-BinD-PCRrep1_I2"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2023-12-05T19:18:34.767960+00:00",
"file_format": "fastq",
"file_size": 2786496,
"href": "/sequence-files/IGVFFI9655VCDB/@@download/IGVFFI9655VCDB.fastq.gz",
"s3_uri": "s3://igvf-files/2023/12/05/e3b44443-0efe-4ddd-a662-e05e63d60d0a/IGVFFI9655VCDB.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_S2-BioRep1-FFRep1-BinD-PCRrep1_S4_I2_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI7610MRKW/",
"accession": "IGVFFI7610MRKW",
"aliases": [
"jesse-engreitz:220829_8merInsertion-Jurkat_NoStimulation-Amp_PPIF_promoter-BioRep1-FFrep1-BinD-PCRrep2_I2"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2023-12-05T19:24:55.525105+00:00",
"file_format": "fastq",
"file_size": 3196799,
"href": "/sequence-files/IGVFFI7610MRKW/@@download/IGVFFI7610MRKW.fastq.gz",
"s3_uri": "s3://igvf-files/2023/12/05/a7ebe8c3-d033-45a4-85a5-540360cd678f/IGVFFI7610MRKW.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_S2-BioRep1-FFRep1-BinD-PCRrep2_S60_I2_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI5240CWOQ/",
"accession": "IGVFFI5240CWOQ",
"aliases": [
"jesse-engreitz:220829_8merInsertion-Jurkat_NoStimulation-Amp_PPIF_promoter-BioRep1-FFrep1-BinD-PCRrep1_I1"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2023-12-05T19:06:06.396619+00:00",
"file_format": "fastq",
"file_size": 2925506,
"href": "/sequence-files/IGVFFI5240CWOQ/@@download/IGVFFI5240CWOQ.fastq.gz",
"s3_uri": "s3://igvf-files/2023/12/05/6f9fca5a-2820-44a2-9319-c0d9bbb9da17/IGVFFI5240CWOQ.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_S2-BioRep1-FFRep1-BinD-PCRrep1_S4_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": "2023-12-20T23:04:58.742812+00:00",
"samples": [
{
"@id": "/in-vitro-systems/IGVFSM2723TUEN/",
"@type": [
"InVitroSystem",
"Biosample",
"Sample",
"Item"
],
"accession": "IGVFSM2723TUEN",
"aliases": [
"jesse-engreitz:220829_8merInsertion-Jurkat_NoStimulation-Amp_PPIF_promoter-BioRep1-FFrep1-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": "2023-12-05T18:40:18.857894+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": "6cbc20a6-5458-4336-ac9e-534d9a8c5704"
}