{
"@context": "/terms/",
"@id": "/measurement-sets/IGVFDS3030YDAT/",
"@type": [
"MeasurementSet",
"FileSet",
"Item"
],
"accession": "IGVFDS3030YDAT",
"aliases": [
"jesse-engreitz:220829_8merInsertion-Jurkat_Stimulation-Amp_PPIF_promoter-BioRep3-FFrep2-BinD_AmpliconSequencing"
],
"assay_term": {
"@id": "/assay-terms/OBI_0003133/",
"term_name": "cas mediated mutagenesis"
},
"audit": {
"INTERNAL_ACTION": [
{
"category": "mismatched status",
"detail": "Released in vitro system [IGVFSM4844JJJX](/in-vitro-systems/IGVFSM4844JJJX/) 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/IGVFSM4844JJJX/"
}
],
"NOT_COMPLIANT": [
{
"category": "missing sequence specification",
"detail": "Measurement set [IGVFDS3030YDAT](/measurement-sets/IGVFDS3030YDAT/) has sequence file(s): [IGVFFI4629OYMM](/sequence-files/IGVFFI4629OYMM/), [IGVFFI4153PMOZ](/sequence-files/IGVFFI4153PMOZ/), [IGVFFI0498WYXK](/sequence-files/IGVFFI0498WYXK/), [IGVFFI0842IMRO](/sequence-files/IGVFFI0842IMRO/), [IGVFFI9472VVFS](/sequence-files/IGVFFI9472VVFS/), [IGVFFI1055BRCU](/sequence-files/IGVFFI1055BRCU/), [IGVFFI3549GFKG](/sequence-files/IGVFFI3549GFKG/), [IGVFFI3359XMWY](/sequence-files/IGVFFI3359XMWY/) which do not have any `seqspecs`. Sequence files in a file set are expected to link to a sequence specification file.",
"level": 50,
"level_name": "NOT_COMPLIANT",
"name": "audit_missing_seqspec",
"path": "/measurement-sets/IGVFDS3030YDAT/"
},
{
"category": "missing auxiliary set",
"detail": "Measurement set [IGVFDS3030YDAT](/measurement-sets/IGVFDS3030YDAT/) 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": 50,
"level_name": "NOT_COMPLIANT",
"name": "audit_CRISPR_assay_missing_cell_sorting_auxiliary_set",
"path": "/measurement-sets/IGVFDS3030YDAT/"
},
{
"category": "missing auxiliary set",
"detail": "Measurement set [IGVFDS3030YDAT](/measurement-sets/IGVFDS3030YDAT/) has no variant sequencing `auxiliary_sets`. Variant FlowFISH measurement sets are expected to link to a variant sequencing auxiliary set.",
"level": 50,
"level_name": "NOT_COMPLIANT",
"name": "audit_Variant_FlowFISH_missing_variant_sequencing_auxiliary_set",
"path": "/measurement-sets/IGVFDS3030YDAT/"
},
{
"category": "missing targeted genes",
"detail": "Measurement set [IGVFDS3030YDAT](/measurement-sets/IGVFDS3030YDAT/) has no `targeted_genes`. ChIP-seq and FISH-based assays are expected to specify targeted gene(s).",
"level": 50,
"level_name": "NOT_COMPLIANT",
"name": "audit_targeted_genes",
"path": "/measurement-sets/IGVFDS3030YDAT/"
}
],
"WARNING": [
{
"category": "missing sequencing kit",
"detail": "Measurement set [IGVFDS3030YDAT](/measurement-sets/IGVFDS3030YDAT/) has sequence file(s) [IGVFFI4629OYMM](/sequence-files/IGVFFI4629OYMM/), [IGVFFI4153PMOZ](/sequence-files/IGVFFI4153PMOZ/), [IGVFFI0498WYXK](/sequence-files/IGVFFI0498WYXK/), [IGVFFI0842IMRO](/sequence-files/IGVFFI0842IMRO/), [IGVFFI9472VVFS](/sequence-files/IGVFFI9472VVFS/), [IGVFFI1055BRCU](/sequence-files/IGVFFI1055BRCU/), [IGVFFI3549GFKG](/sequence-files/IGVFFI3549GFKG/), [IGVFFI3359XMWY](/sequence-files/IGVFFI3359XMWY/) which lack specification of a `sequencing_kit`. Sequence files should specify a sequencing kit.",
"level": 40,
"level_name": "WARNING",
"name": "audit_inconsistent_sequencing_kit",
"path": "/measurement-sets/IGVFDS3030YDAT/"
}
]
},
"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"
]
}
],
"control_for": [],
"creation_timestamp": "2023-11-30T22:48:29.172183+00:00",
"donors": [
{
"@id": "/human-donors/IGVFDO1080XFGV/",
"accession": "IGVFDO1080XFGV",
"aliases": [
"igvf:donor_of_Jurkat"
],
"sex": "male",
"status": "released",
"taxa": "Homo sapiens"
}
],
"file_set_type": "experimental data",
"files": [
{
"@id": "/sequence-files/IGVFFI4629OYMM/",
"accession": "IGVFFI4629OYMM",
"aliases": [
"jesse-engreitz:220829_8merInsertion-Jurkat_Stimulation-Amp_PPIF_promoter-BioRep3-FFrep2-BinD-PCRrep1_R1"
],
"content_type": "reads",
"creation_timestamp": "2023-12-05T19:36:24.517218+00:00",
"file_format": "fastq",
"file_size": 7425974,
"href": "/sequence-files/IGVFFI4629OYMM/@@download/IGVFFI4629OYMM.fastq.gz",
"s3_uri": "s3://igvf-files/2023/12/05/1b12f7e7-96f8-47a8-ab7e-806bea61b002/IGVFFI4629OYMM.fastq.gz",
"sequencing_platform": {
"@id": "/platform-terms/EFO_0008566/",
"term_name": "Illumina NextSeq 550"
},
"submitted_file_name": "220829_pPPIF_JurkatVFF-Jurkat-PE2A-BFP-pPPIF-Amp_pPPIF2_S18-BioRep3-FFRep2-BinD-PCRrep1_S151_R1_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI4153PMOZ/",
"accession": "IGVFFI4153PMOZ",
"aliases": [
"jesse-engreitz:220829_8merInsertion-Jurkat_Stimulation-Amp_PPIF_promoter-BioRep3-FFrep2-BinD-PCRrep1_R2"
],
"content_type": "reads",
"creation_timestamp": "2023-12-05T19:44:52.457918+00:00",
"file_format": "fastq",
"file_size": 13920546,
"href": "/sequence-files/IGVFFI4153PMOZ/@@download/IGVFFI4153PMOZ.fastq.gz",
"s3_uri": "s3://igvf-files/2023/12/05/028d35e1-6e49-492b-9d7e-0af8280386dc/IGVFFI4153PMOZ.fastq.gz",
"sequencing_platform": {
"@id": "/platform-terms/EFO_0008566/",
"term_name": "Illumina NextSeq 550"
},
"submitted_file_name": "220829_pPPIF_JurkatVFF-Jurkat-PE2A-BFP-pPPIF-Amp_pPPIF2_S18-BioRep3-FFRep2-BinD-PCRrep1_S151_R2_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI0498WYXK/",
"accession": "IGVFFI0498WYXK",
"aliases": [
"jesse-engreitz:220829_8merInsertion-Jurkat_Stimulation-Amp_PPIF_promoter-BioRep3-FFrep2-BinD-PCRrep1_I1"
],
"content_type": "reads",
"creation_timestamp": "2023-12-05T19:53:14.077499+00:00",
"file_format": "fastq",
"file_size": 3300288,
"href": "/sequence-files/IGVFFI0498WYXK/@@download/IGVFFI0498WYXK.fastq.gz",
"s3_uri": "s3://igvf-files/2023/12/05/c03707f6-87cd-4680-b807-e6669a0b68fb/IGVFFI0498WYXK.fastq.gz",
"sequencing_platform": {
"@id": "/platform-terms/EFO_0008566/",
"term_name": "Illumina NextSeq 550"
},
"submitted_file_name": "220829_pPPIF_JurkatVFF-Jurkat-PE2A-BFP-pPPIF-Amp_pPPIF2_S18-BioRep3-FFRep2-BinD-PCRrep1_S151_I1_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI0842IMRO/",
"accession": "IGVFFI0842IMRO",
"aliases": [
"jesse-engreitz:220829_8merInsertion-Jurkat_Stimulation-Amp_PPIF_promoter-BioRep3-FFrep2-BinD-PCRrep1_I2"
],
"content_type": "reads",
"creation_timestamp": "2023-12-05T20:01:21.388775+00:00",
"file_format": "fastq",
"file_size": 3116004,
"href": "/sequence-files/IGVFFI0842IMRO/@@download/IGVFFI0842IMRO.fastq.gz",
"s3_uri": "s3://igvf-files/2023/12/05/07d344d2-5a1c-4837-8567-2fb091c46b3f/IGVFFI0842IMRO.fastq.gz",
"sequencing_platform": {
"@id": "/platform-terms/EFO_0008566/",
"term_name": "Illumina NextSeq 550"
},
"submitted_file_name": "220829_pPPIF_JurkatVFF-Jurkat-PE2A-BFP-pPPIF-Amp_pPPIF2_S18-BioRep3-FFRep2-BinD-PCRrep1_S151_I2_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI9472VVFS/",
"accession": "IGVFFI9472VVFS",
"aliases": [
"jesse-engreitz:220829_8merInsertion-Jurkat_Stimulation-Amp_PPIF_promoter-BioRep3-FFrep2-BinD-PCRrep2_R1"
],
"content_type": "reads",
"creation_timestamp": "2023-12-05T20:09:35.592580+00:00",
"file_format": "fastq",
"file_size": 7829063,
"href": "/sequence-files/IGVFFI9472VVFS/@@download/IGVFFI9472VVFS.fastq.gz",
"s3_uri": "s3://igvf-files/2023/12/05/49634226-7161-4c3f-a547-f36a31ba4446/IGVFFI9472VVFS.fastq.gz",
"sequencing_platform": {
"@id": "/platform-terms/EFO_0008566/",
"term_name": "Illumina NextSeq 550"
},
"submitted_file_name": "220829_pPPIF_JurkatVFF-Jurkat-PE2A-BFP-pPPIF-Amp_pPPIF2_S18-BioRep3-FFRep2-BinD-PCRrep2_S208_R1_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI1055BRCU/",
"accession": "IGVFFI1055BRCU",
"aliases": [
"jesse-engreitz:220829_8merInsertion-Jurkat_Stimulation-Amp_PPIF_promoter-BioRep3-FFrep2-BinD-PCRrep2_R2"
],
"content_type": "reads",
"creation_timestamp": "2023-12-05T20:18:03.747922+00:00",
"file_format": "fastq",
"file_size": 14571209,
"href": "/sequence-files/IGVFFI1055BRCU/@@download/IGVFFI1055BRCU.fastq.gz",
"s3_uri": "s3://igvf-files/2023/12/05/ff5aa3f3-b6b3-49d1-9067-0d2ddcc64388/IGVFFI1055BRCU.fastq.gz",
"sequencing_platform": {
"@id": "/platform-terms/EFO_0008566/",
"term_name": "Illumina NextSeq 550"
},
"submitted_file_name": "220829_pPPIF_JurkatVFF-Jurkat-PE2A-BFP-pPPIF-Amp_pPPIF2_S18-BioRep3-FFRep2-BinD-PCRrep2_S208_R2_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI3549GFKG/",
"accession": "IGVFFI3549GFKG",
"aliases": [
"jesse-engreitz:220829_8merInsertion-Jurkat_Stimulation-Amp_PPIF_promoter-BioRep3-FFrep2-BinD-PCRrep2_I1"
],
"content_type": "reads",
"creation_timestamp": "2023-12-05T20:26:27.381234+00:00",
"file_format": "fastq",
"file_size": 3415292,
"href": "/sequence-files/IGVFFI3549GFKG/@@download/IGVFFI3549GFKG.fastq.gz",
"s3_uri": "s3://igvf-files/2023/12/05/c46bd23b-b0a9-48b9-bfcc-dfe357945964/IGVFFI3549GFKG.fastq.gz",
"sequencing_platform": {
"@id": "/platform-terms/EFO_0008566/",
"term_name": "Illumina NextSeq 550"
},
"submitted_file_name": "220829_pPPIF_JurkatVFF-Jurkat-PE2A-BFP-pPPIF-Amp_pPPIF2_S18-BioRep3-FFRep2-BinD-PCRrep2_S208_I1_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI3359XMWY/",
"accession": "IGVFFI3359XMWY",
"aliases": [
"jesse-engreitz:220829_8merInsertion-Jurkat_Stimulation-Amp_PPIF_promoter-BioRep3-FFrep2-BinD-PCRrep2_I2"
],
"content_type": "reads",
"creation_timestamp": "2023-12-05T20:34:40.477818+00:00",
"file_format": "fastq",
"file_size": 3265095,
"href": "/sequence-files/IGVFFI3359XMWY/@@download/IGVFFI3359XMWY.fastq.gz",
"s3_uri": "s3://igvf-files/2023/12/05/bb8824e2-524d-44ab-9812-89fa5d43894a/IGVFFI3359XMWY.fastq.gz",
"sequencing_platform": {
"@id": "/platform-terms/EFO_0008566/",
"term_name": "Illumina NextSeq 550"
},
"submitted_file_name": "220829_pPPIF_JurkatVFF-Jurkat-PE2A-BFP-pPPIF-Amp_pPPIF2_S18-BioRep3-FFRep2-BinD-PCRrep2_S208_I2_001.fastq.gz",
"upload_status": "validated"
}
],
"input_file_set_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.",
"preferred_assay_title": "Variant FlowFISH",
"protocols": [
"https://www.protocols.io/view/flowfish-with-primeflow-36wgq3q4olk5/v1"
],
"release_timestamp": "2023-12-20T23:04:25.476875+00:00",
"samples": [
{
"@id": "/in-vitro-systems/IGVFSM4844JJJX/",
"@type": [
"InVitroSystem",
"Biosample",
"Sample",
"Item"
],
"accession": "IGVFSM4844JJJX",
"aliases": [
"jesse-engreitz:220829_8merInsertion-Jurkat_Stimulation-Amp_PPIF_promoter-BioRep3-FFrep2-BinD"
],
"classifications": [
"cell line"
],
"construct_library_sets": [
{
"@id": "/construct-library-sets/IGVFDS6377KNCH/",
"accession": "IGVFDS6377KNCH",
"file_set_type": "guide library",
"summary": "Guide (sgRNA) library targeting sequence variants in a genomic locus"
}
],
"modifications": [
{
"@id": "/crispr-modifications/fc6bc0b3-a064-47d0-b95d-a9af14bb1624/",
"modality": "prime editing"
}
],
"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) 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 a guide library",
"taxa": "Homo sapiens",
"treatments": [
{
"@id": "/treatments/df02c0d4-f796-4f77-bfbc-388cdbfcc615/",
"purpose": "stimulation",
"summary": "Treatment of 5 μg/mL T-cell surface glycoprotein CD3 gamma chain for 4 hours",
"treatment_type": "protein"
},
{
"@id": "/treatments/42b3c61d-38de-4bd2-bb39-33c125a417cb/",
"purpose": "stimulation",
"summary": "Treatment of 100 ng/mL phorbol 13-acetate 12-myristate for 4 hours",
"treatment_type": "chemical"
}
]
}
],
"schema_version": "17",
"status": "released",
"submitted_by": {
"@id": "/users/f9e7cd82-a407-4a20-89ee-f4dc668b0cbe/",
"title": "Michael Montgomery"
},
"submitted_files_timestamp": "2023-12-05T19:36:24.517218+00:00",
"summary": "cas mediated mutagenesis (Variant FlowFISH) integrating a guide (sgRNA) library targeting sequence variants in a genomic locus",
"uuid": "c668d941-4a5b-491e-b035-772b3be524d6"
}