{
"@context": "/terms/",
"@id": "/measurement-sets/IGVFDS4515XTAP/",
"@type": [
"MeasurementSet",
"FileSet",
"Item"
],
"accession": "IGVFDS4515XTAP",
"aliases": [
"jesse-engreitz:220829_8merInsertion-Jurkat_Stimulation-Amp_PPIF_promoter-BioRep4-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 [IGVFDS4515XTAP](/measurement-sets/IGVFDS4515XTAP/) has sequence file(s) [IGVFFI9579LZMX](/sequence-files/IGVFFI9579LZMX/), [IGVFFI4521BKLA](/sequence-files/IGVFFI4521BKLA/), [IGVFFI8937OFSJ](/sequence-files/IGVFFI8937OFSJ/), [IGVFFI1808LDFO](/sequence-files/IGVFFI1808LDFO/), [IGVFFI1026PKON](/sequence-files/IGVFFI1026PKON/), [IGVFFI5567CLXY](/sequence-files/IGVFFI5567CLXY/), [IGVFFI2051MUKE](/sequence-files/IGVFFI2051MUKE/), [IGVFFI0752RXDQ](/sequence-files/IGVFFI0752RXDQ/) 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/IGVFDS4515XTAP/"
},
{
"category": "missing sequence specification",
"detail": "Measurement set [IGVFDS4515XTAP](/measurement-sets/IGVFDS4515XTAP/) has sequence file(s): [IGVFFI9579LZMX](/sequence-files/IGVFFI9579LZMX/), [IGVFFI4521BKLA](/sequence-files/IGVFFI4521BKLA/), [IGVFFI8937OFSJ](/sequence-files/IGVFFI8937OFSJ/), [IGVFFI1808LDFO](/sequence-files/IGVFFI1808LDFO/), [IGVFFI1026PKON](/sequence-files/IGVFFI1026PKON/), [IGVFFI5567CLXY](/sequence-files/IGVFFI5567CLXY/), [IGVFFI2051MUKE](/sequence-files/IGVFFI2051MUKE/), [IGVFFI0752RXDQ](/sequence-files/IGVFFI0752RXDQ/) 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/IGVFDS4515XTAP/"
},
{
"category": "mismatched status",
"detail": "Released in vitro system [IGVFSM0453ERNS](/in-vitro-systems/IGVFSM0453ERNS/) 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/IGVFSM0453ERNS/"
}
],
"WARNING": [
{
"category": "missing auxiliary set",
"detail": "Measurement set [IGVFDS4515XTAP](/measurement-sets/IGVFDS4515XTAP/) 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/IGVFDS4515XTAP/"
}
]
},
"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": "2023-11-30T22:48:45.482065+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/IGVFFI9579LZMX/",
"accession": "IGVFFI9579LZMX",
"aliases": [
"jesse-engreitz:220829_8merInsertion-Jurkat_Stimulation-Amp_PPIF_promoter-BioRep4-FFrep2-BinE-PCRrep1_I1"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2023-12-05T19:55:24.743779+00:00",
"file_format": "fastq",
"file_size": 3403973,
"href": "/sequence-files/IGVFFI9579LZMX/@@download/IGVFFI9579LZMX.fastq.gz",
"s3_uri": "s3://igvf-files/2023/12/05/e75d9dcf-0147-438e-8604-9c774dd7cff6/IGVFFI9579LZMX.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_pPPIF2_S20-BioRep4-FFRep2-BinE-PCRrep1_S166_I1_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI4521BKLA/",
"accession": "IGVFFI4521BKLA",
"aliases": [
"jesse-engreitz:220829_8merInsertion-Jurkat_Stimulation-Amp_PPIF_promoter-BioRep4-FFrep2-BinE-PCRrep2_I2"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2023-12-05T20:36:51.173101+00:00",
"file_format": "fastq",
"file_size": 3117699,
"href": "/sequence-files/IGVFFI4521BKLA/@@download/IGVFFI4521BKLA.fastq.gz",
"s3_uri": "s3://igvf-files/2023/12/05/418003e4-083d-4c03-8a2d-363ca9af799f/IGVFFI4521BKLA.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_pPPIF2_S20-BioRep4-FFRep2-BinE-PCRrep2_S223_I2_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI8937OFSJ/",
"accession": "IGVFFI8937OFSJ",
"aliases": [
"jesse-engreitz:220829_8merInsertion-Jurkat_Stimulation-Amp_PPIF_promoter-BioRep4-FFrep2-BinE-PCRrep2_R2"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2023-12-05T20:20:20.679194+00:00",
"file_format": "fastq",
"file_size": 13854609,
"href": "/sequence-files/IGVFFI8937OFSJ/@@download/IGVFFI8937OFSJ.fastq.gz",
"s3_uri": "s3://igvf-files/2023/12/05/68daf5ea-6119-450c-a6bb-fa47d1af4d6e/IGVFFI8937OFSJ.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_pPPIF2_S20-BioRep4-FFRep2-BinE-PCRrep2_S223_R2_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI1808LDFO/",
"accession": "IGVFFI1808LDFO",
"aliases": [
"jesse-engreitz:220829_8merInsertion-Jurkat_Stimulation-Amp_PPIF_promoter-BioRep4-FFrep2-BinE-PCRrep1_R1"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2023-12-05T19:38:37.437636+00:00",
"file_format": "fastq",
"file_size": 8030667,
"href": "/sequence-files/IGVFFI1808LDFO/@@download/IGVFFI1808LDFO.fastq.gz",
"s3_uri": "s3://igvf-files/2023/12/05/7732795f-cda1-42e8-a170-3897fec8b86d/IGVFFI1808LDFO.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_pPPIF2_S20-BioRep4-FFRep2-BinE-PCRrep1_S166_R1_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI1026PKON/",
"accession": "IGVFFI1026PKON",
"aliases": [
"jesse-engreitz:220829_8merInsertion-Jurkat_Stimulation-Amp_PPIF_promoter-BioRep4-FFrep2-BinE-PCRrep1_R2"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2023-12-05T19:47:09.627263+00:00",
"file_format": "fastq",
"file_size": 14923912,
"href": "/sequence-files/IGVFFI1026PKON/@@download/IGVFFI1026PKON.fastq.gz",
"s3_uri": "s3://igvf-files/2023/12/05/011c0189-877c-4d13-b798-9e8cbd4a7ea0/IGVFFI1026PKON.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_pPPIF2_S20-BioRep4-FFRep2-BinE-PCRrep1_S166_R2_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI5567CLXY/",
"accession": "IGVFFI5567CLXY",
"aliases": [
"jesse-engreitz:220829_8merInsertion-Jurkat_Stimulation-Amp_PPIF_promoter-BioRep4-FFrep2-BinE-PCRrep2_R1"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2023-12-05T20:11:48.723453+00:00",
"file_format": "fastq",
"file_size": 7447942,
"href": "/sequence-files/IGVFFI5567CLXY/@@download/IGVFFI5567CLXY.fastq.gz",
"s3_uri": "s3://igvf-files/2023/12/05/c4f88ae4-3721-4cbe-8f21-0849de50cb4d/IGVFFI5567CLXY.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_pPPIF2_S20-BioRep4-FFRep2-BinE-PCRrep2_S223_R1_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI2051MUKE/",
"accession": "IGVFFI2051MUKE",
"aliases": [
"jesse-engreitz:220829_8merInsertion-Jurkat_Stimulation-Amp_PPIF_promoter-BioRep4-FFrep2-BinE-PCRrep1_I2"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2023-12-05T20:03:31.895424+00:00",
"file_format": "fastq",
"file_size": 3360994,
"href": "/sequence-files/IGVFFI2051MUKE/@@download/IGVFFI2051MUKE.fastq.gz",
"s3_uri": "s3://igvf-files/2023/12/05/2232a376-a8ac-4225-b119-a0f2ab3085d6/IGVFFI2051MUKE.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_pPPIF2_S20-BioRep4-FFRep2-BinE-PCRrep1_S166_I2_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI0752RXDQ/",
"accession": "IGVFFI0752RXDQ",
"aliases": [
"jesse-engreitz:220829_8merInsertion-Jurkat_Stimulation-Amp_PPIF_promoter-BioRep4-FFrep2-BinE-PCRrep2_I1"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2023-12-05T20:28:38.535417+00:00",
"file_format": "fastq",
"file_size": 3357518,
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"s3_uri": "s3://igvf-files/2023/12/05/4690ec35-c5d8-4e2e-9727-fab3d70dfe2d/IGVFFI0752RXDQ.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_pPPIF2_S20-BioRep4-FFRep2-BinE-PCRrep2_S223_I1_001.fastq.gz",
"upload_status": "validated"
}
],
"input_for": [
"/analysis-sets/IGVFDS1863TJOE/"
],
"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": "2023-12-20T23:04:23.019524+00:00",
"samples": [
{
"@id": "/in-vitro-systems/IGVFSM0453ERNS/",
"@type": [
"InVitroSystem",
"Biosample",
"Sample",
"Item"
],
"accession": "IGVFSM0453ERNS",
"aliases": [
"jesse-engreitz:220829_8merInsertion-Jurkat_Stimulation-Amp_PPIF_promoter-BioRep4-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) treated with 100 ng/mL phorbol 13-acetate 12-myristate for 4 hours, 5 μg/mL T-cell surface glycoprotein CD3 gamma chain for 4 hours, modified with CRISPR prime editing Sp-nCas9-M-MLV RT (PE2), transfected with a guide library",
"taxa": "Homo sapiens",
"treatments": [
{
"@id": "/treatments/df02c0d4-f796-4f77-bfbc-388cdbfcc615/",
"status": "released",
"treatment_term_name": "T-cell surface glycoprotein CD3 gamma chain"
},
{
"@id": "/treatments/42b3c61d-38de-4bd2-bb39-33c125a417cb/",
"status": "released",
"treatment_term_name": "phorbol 13-acetate 12-myristate"
}
]
}
],
"schema_version": "23",
"status": "released",
"submitted_by": {
"@id": "/users/f9e7cd82-a407-4a20-89ee-f4dc668b0cbe/",
"title": "Michael Montgomery"
},
"submitted_files_timestamp": "2023-12-05T19:38:37.437636+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": "c5aafa51-5106-4436-9ffc-5d50c169196d"
}