{
"@context": "/terms/",
"@id": "/measurement-sets/IGVFDS3553DWNL/",
"@type": [
"MeasurementSet",
"FileSet",
"Item"
],
"accession": "IGVFDS3553DWNL",
"aliases": [
"jesse-engreitz:220829_8merInsertion-Jurkat_Stimulation-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": "mismatched status",
"detail": "Released in vitro system [IGVFSM3105OTRY](/in-vitro-systems/IGVFSM3105OTRY/) 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/IGVFSM3105OTRY/"
},
{
"category": "missing sequencing kit",
"detail": "Measurement set [IGVFDS3553DWNL](/measurement-sets/IGVFDS3553DWNL/) has sequence file(s) [IGVFFI8180HLAX](/sequence-files/IGVFFI8180HLAX/), [IGVFFI2270QFFQ](/sequence-files/IGVFFI2270QFFQ/), [IGVFFI1138BEVY](/sequence-files/IGVFFI1138BEVY/), [IGVFFI2457RSJQ](/sequence-files/IGVFFI2457RSJQ/), [IGVFFI4752OAZF](/sequence-files/IGVFFI4752OAZF/), [IGVFFI0222UTFK](/sequence-files/IGVFFI0222UTFK/), [IGVFFI0402AEUG](/sequence-files/IGVFFI0402AEUG/), [IGVFFI2022GLIW](/sequence-files/IGVFFI2022GLIW/) 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/IGVFDS3553DWNL/"
},
{
"category": "missing sequence specification",
"detail": "Measurement set [IGVFDS3553DWNL](/measurement-sets/IGVFDS3553DWNL/) has sequence file(s): [IGVFFI8180HLAX](/sequence-files/IGVFFI8180HLAX/), [IGVFFI2270QFFQ](/sequence-files/IGVFFI2270QFFQ/), [IGVFFI1138BEVY](/sequence-files/IGVFFI1138BEVY/), [IGVFFI2457RSJQ](/sequence-files/IGVFFI2457RSJQ/), [IGVFFI4752OAZF](/sequence-files/IGVFFI4752OAZF/), [IGVFFI0222UTFK](/sequence-files/IGVFFI0222UTFK/), [IGVFFI0402AEUG](/sequence-files/IGVFFI0402AEUG/), [IGVFFI2022GLIW](/sequence-files/IGVFFI2022GLIW/) 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/IGVFDS3553DWNL/"
}
],
"WARNING": [
{
"category": "missing auxiliary set",
"detail": "Measurement set [IGVFDS3553DWNL](/measurement-sets/IGVFDS3553DWNL/) 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/IGVFDS3553DWNL/"
}
]
},
"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": "2023-11-30T22:48:30.222973+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/IGVFFI8180HLAX/",
"accession": "IGVFFI8180HLAX",
"aliases": [
"jesse-engreitz:220829_8merInsertion-Jurkat_Stimulation-Amp_PPIF_promoter-BioRep3-FFrep2-BinE-PCRrep1_I2"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2023-12-05T20:01:29.993282+00:00",
"file_format": "fastq",
"file_size": 3121212,
"href": "/sequence-files/IGVFFI8180HLAX/@@download/IGVFFI8180HLAX.fastq.gz",
"s3_uri": "s3://igvf-files/2023/12/05/2c8d2454-9c82-4281-9523-ece5da249b58/IGVFFI8180HLAX.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_S18-BioRep3-FFRep2-BinE-PCRrep1_S152_I2_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI2270QFFQ/",
"accession": "IGVFFI2270QFFQ",
"aliases": [
"jesse-engreitz:220829_8merInsertion-Jurkat_Stimulation-Amp_PPIF_promoter-BioRep3-FFrep2-BinE-PCRrep2_R2"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2023-12-05T20:18:12.908515+00:00",
"file_format": "fastq",
"file_size": 14607690,
"href": "/sequence-files/IGVFFI2270QFFQ/@@download/IGVFFI2270QFFQ.fastq.gz",
"s3_uri": "s3://igvf-files/2023/12/05/cb8a8815-d989-4502-9461-df1f022cd21e/IGVFFI2270QFFQ.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_S18-BioRep3-FFRep2-BinE-PCRrep2_S209_R2_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI1138BEVY/",
"accession": "IGVFFI1138BEVY",
"aliases": [
"jesse-engreitz:220829_8merInsertion-Jurkat_Stimulation-Amp_PPIF_promoter-BioRep3-FFrep2-BinE-PCRrep1_R2"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2023-12-05T19:45:01.710489+00:00",
"file_format": "fastq",
"file_size": 13938999,
"href": "/sequence-files/IGVFFI1138BEVY/@@download/IGVFFI1138BEVY.fastq.gz",
"s3_uri": "s3://igvf-files/2023/12/05/2f7829a9-59b0-4c0c-a188-f11eb4d1a84e/IGVFFI1138BEVY.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_S18-BioRep3-FFRep2-BinE-PCRrep1_S152_R2_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI2457RSJQ/",
"accession": "IGVFFI2457RSJQ",
"aliases": [
"jesse-engreitz:220829_8merInsertion-Jurkat_Stimulation-Amp_PPIF_promoter-BioRep3-FFrep2-BinE-PCRrep1_R1"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2023-12-05T19:36:33.501514+00:00",
"file_format": "fastq",
"file_size": 7418777,
"href": "/sequence-files/IGVFFI2457RSJQ/@@download/IGVFFI2457RSJQ.fastq.gz",
"s3_uri": "s3://igvf-files/2023/12/05/b26eca68-b8d7-460a-8bf5-7fb3086a713d/IGVFFI2457RSJQ.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_S18-BioRep3-FFRep2-BinE-PCRrep1_S152_R1_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI4752OAZF/",
"accession": "IGVFFI4752OAZF",
"aliases": [
"jesse-engreitz:220829_8merInsertion-Jurkat_Stimulation-Amp_PPIF_promoter-BioRep3-FFrep2-BinE-PCRrep2_R1"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2023-12-05T20:09:44.468321+00:00",
"file_format": "fastq",
"file_size": 7897636,
"href": "/sequence-files/IGVFFI4752OAZF/@@download/IGVFFI4752OAZF.fastq.gz",
"s3_uri": "s3://igvf-files/2023/12/05/73aa9f80-923a-4003-afff-c5be6927f457/IGVFFI4752OAZF.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_S18-BioRep3-FFRep2-BinE-PCRrep2_S209_R1_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI0222UTFK/",
"accession": "IGVFFI0222UTFK",
"aliases": [
"jesse-engreitz:220829_8merInsertion-Jurkat_Stimulation-Amp_PPIF_promoter-BioRep3-FFrep2-BinE-PCRrep1_I1"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2023-12-05T19:53:22.719506+00:00",
"file_format": "fastq",
"file_size": 3160984,
"href": "/sequence-files/IGVFFI0222UTFK/@@download/IGVFFI0222UTFK.fastq.gz",
"s3_uri": "s3://igvf-files/2023/12/05/bac1bc19-1f11-4542-a97e-5508a20c0aa5/IGVFFI0222UTFK.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_S18-BioRep3-FFRep2-BinE-PCRrep1_S152_I1_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI0402AEUG/",
"accession": "IGVFFI0402AEUG",
"aliases": [
"jesse-engreitz:220829_8merInsertion-Jurkat_Stimulation-Amp_PPIF_promoter-BioRep3-FFrep2-BinE-PCRrep2_I1"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2023-12-05T20:26:36.033117+00:00",
"file_format": "fastq",
"file_size": 3280973,
"href": "/sequence-files/IGVFFI0402AEUG/@@download/IGVFFI0402AEUG.fastq.gz",
"s3_uri": "s3://igvf-files/2023/12/05/1fcf818a-0fa9-4909-9f1f-ca7bc58165e7/IGVFFI0402AEUG.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_S18-BioRep3-FFRep2-BinE-PCRrep2_S209_I1_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI2022GLIW/",
"accession": "IGVFFI2022GLIW",
"aliases": [
"jesse-engreitz:220829_8merInsertion-Jurkat_Stimulation-Amp_PPIF_promoter-BioRep3-FFrep2-BinE-PCRrep2_I2"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2023-12-05T20:34:49.189520+00:00",
"file_format": "fastq",
"file_size": 3310630,
"href": "/sequence-files/IGVFFI2022GLIW/@@download/IGVFFI2022GLIW.fastq.gz",
"s3_uri": "s3://igvf-files/2023/12/05/40fefbe6-da63-4037-8824-cbf57b5bb6c7/IGVFFI2022GLIW.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_S18-BioRep3-FFRep2-BinE-PCRrep2_S209_I2_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": "2023-12-20T23:03:58.848787+00:00",
"samples": [
{
"@id": "/in-vitro-systems/IGVFSM3105OTRY/",
"@type": [
"InVitroSystem",
"Biosample",
"Sample",
"Item"
],
"accession": "IGVFSM3105OTRY",
"aliases": [
"jesse-engreitz:220829_8merInsertion-Jurkat_Stimulation-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) 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": "2023-12-05T19:36:33.501514+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": "caad1c64-6fa1-488f-9044-ff275d237865"
}