{
"@context": "/terms/",
"@id": "/measurement-sets/IGVFDS2192NCTH/",
"@type": [
"MeasurementSet",
"FileSet",
"Item"
],
"accession": "IGVFDS2192NCTH",
"aliases": [
"jesse-engreitz:220829_8merInsertion-Jurkat_Stimulation-Amp_PPIF_promoter-BioRep2-FFrep1-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 [IGVFSM4221WRQS](/in-vitro-systems/IGVFSM4221WRQS/) 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/IGVFSM4221WRQS/"
}
],
"NOT_COMPLIANT": [
{
"category": "missing sequence specification",
"detail": "Measurement set [IGVFDS2192NCTH](/measurement-sets/IGVFDS2192NCTH/) has sequence file(s): [IGVFFI5305PVWV](/sequence-files/IGVFFI5305PVWV/), [IGVFFI5476FOPQ](/sequence-files/IGVFFI5476FOPQ/), [IGVFFI3349WKOP](/sequence-files/IGVFFI3349WKOP/), [IGVFFI1165AJSO](/sequence-files/IGVFFI1165AJSO/), [IGVFFI6649IDBY](/sequence-files/IGVFFI6649IDBY/), [IGVFFI1854RBAF](/sequence-files/IGVFFI1854RBAF/), [IGVFFI8749BGVD](/sequence-files/IGVFFI8749BGVD/), [IGVFFI2200CONX](/sequence-files/IGVFFI2200CONX/) 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/IGVFDS2192NCTH/"
},
{
"category": "missing auxiliary set",
"detail": "Measurement set [IGVFDS2192NCTH](/measurement-sets/IGVFDS2192NCTH/) 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/IGVFDS2192NCTH/"
},
{
"category": "missing auxiliary set",
"detail": "Measurement set [IGVFDS2192NCTH](/measurement-sets/IGVFDS2192NCTH/) 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/IGVFDS2192NCTH/"
},
{
"category": "missing targeted genes",
"detail": "Measurement set [IGVFDS2192NCTH](/measurement-sets/IGVFDS2192NCTH/) 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/IGVFDS2192NCTH/"
}
],
"WARNING": [
{
"category": "missing sequencing kit",
"detail": "Measurement set [IGVFDS2192NCTH](/measurement-sets/IGVFDS2192NCTH/) has sequence file(s) [IGVFFI5305PVWV](/sequence-files/IGVFFI5305PVWV/), [IGVFFI5476FOPQ](/sequence-files/IGVFFI5476FOPQ/), [IGVFFI3349WKOP](/sequence-files/IGVFFI3349WKOP/), [IGVFFI1165AJSO](/sequence-files/IGVFFI1165AJSO/), [IGVFFI6649IDBY](/sequence-files/IGVFFI6649IDBY/), [IGVFFI1854RBAF](/sequence-files/IGVFFI1854RBAF/), [IGVFFI8749BGVD](/sequence-files/IGVFFI8749BGVD/), [IGVFFI2200CONX](/sequence-files/IGVFFI2200CONX/) 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/IGVFDS2192NCTH/"
}
]
},
"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": "2023-11-30T22:48:06.065303+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/IGVFFI5305PVWV/",
"accession": "IGVFFI5305PVWV",
"aliases": [
"jesse-engreitz:220829_8merInsertion-Jurkat_Stimulation-Amp_PPIF_promoter-BioRep2-FFrep1-BinD-PCRrep1_R1"
],
"content_type": "reads",
"creation_timestamp": "2023-12-05T19:33:18.204741+00:00",
"file_format": "fastq",
"file_size": 7326838,
"href": "/sequence-files/IGVFFI5305PVWV/@@download/IGVFFI5305PVWV.fastq.gz",
"s3_uri": "s3://igvf-files/2023/12/05/891bd198-e987-431e-9e26-4a1ba02a3657/IGVFFI5305PVWV.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_S15-BioRep2-FFRep1-BinD-PCRrep1_S130_R1_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI5476FOPQ/",
"accession": "IGVFFI5476FOPQ",
"aliases": [
"jesse-engreitz:220829_8merInsertion-Jurkat_Stimulation-Amp_PPIF_promoter-BioRep2-FFrep1-BinD-PCRrep1_R2"
],
"content_type": "reads",
"creation_timestamp": "2023-12-05T19:41:40.421062+00:00",
"file_format": "fastq",
"file_size": 13591326,
"href": "/sequence-files/IGVFFI5476FOPQ/@@download/IGVFFI5476FOPQ.fastq.gz",
"s3_uri": "s3://igvf-files/2023/12/05/d234f289-66d5-4ef3-bc57-5da57cc2363c/IGVFFI5476FOPQ.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_S15-BioRep2-FFRep1-BinD-PCRrep1_S130_R2_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI3349WKOP/",
"accession": "IGVFFI3349WKOP",
"aliases": [
"jesse-engreitz:220829_8merInsertion-Jurkat_Stimulation-Amp_PPIF_promoter-BioRep2-FFrep1-BinD-PCRrep1_I1"
],
"content_type": "reads",
"creation_timestamp": "2023-12-05T19:50:10.916878+00:00",
"file_format": "fastq",
"file_size": 3094968,
"href": "/sequence-files/IGVFFI3349WKOP/@@download/IGVFFI3349WKOP.fastq.gz",
"s3_uri": "s3://igvf-files/2023/12/05/b2e812d3-8fd0-42fb-b021-caf59f2a94c1/IGVFFI3349WKOP.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_S15-BioRep2-FFRep1-BinD-PCRrep1_S130_I1_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI1165AJSO/",
"accession": "IGVFFI1165AJSO",
"aliases": [
"jesse-engreitz:220829_8merInsertion-Jurkat_Stimulation-Amp_PPIF_promoter-BioRep2-FFrep1-BinD-PCRrep1_I2"
],
"content_type": "reads",
"creation_timestamp": "2023-12-05T19:58:18.462157+00:00",
"file_format": "fastq",
"file_size": 3060311,
"href": "/sequence-files/IGVFFI1165AJSO/@@download/IGVFFI1165AJSO.fastq.gz",
"s3_uri": "s3://igvf-files/2023/12/05/fffcd64e-af02-4675-8953-7352459ee06a/IGVFFI1165AJSO.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_S15-BioRep2-FFRep1-BinD-PCRrep1_S130_I2_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI6649IDBY/",
"accession": "IGVFFI6649IDBY",
"aliases": [
"jesse-engreitz:220829_8merInsertion-Jurkat_Stimulation-Amp_PPIF_promoter-BioRep2-FFrep1-BinD-PCRrep2_R1"
],
"content_type": "reads",
"creation_timestamp": "2023-12-05T20:06:30.353713+00:00",
"file_format": "fastq",
"file_size": 7666433,
"href": "/sequence-files/IGVFFI6649IDBY/@@download/IGVFFI6649IDBY.fastq.gz",
"s3_uri": "s3://igvf-files/2023/12/05/fd5b4894-a7fb-4d6c-bb52-d1d60bcab392/IGVFFI6649IDBY.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_S15-BioRep2-FFRep1-BinD-PCRrep2_S187_R1_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI1854RBAF/",
"accession": "IGVFFI1854RBAF",
"aliases": [
"jesse-engreitz:220829_8merInsertion-Jurkat_Stimulation-Amp_PPIF_promoter-BioRep2-FFrep1-BinD-PCRrep2_R2"
],
"content_type": "reads",
"creation_timestamp": "2023-12-05T20:14:50.900707+00:00",
"file_format": "fastq",
"file_size": 14206284,
"href": "/sequence-files/IGVFFI1854RBAF/@@download/IGVFFI1854RBAF.fastq.gz",
"s3_uri": "s3://igvf-files/2023/12/05/2b17aaec-063c-4139-aea6-61644ff26122/IGVFFI1854RBAF.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_S15-BioRep2-FFRep1-BinD-PCRrep2_S187_R2_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI8749BGVD/",
"accession": "IGVFFI8749BGVD",
"aliases": [
"jesse-engreitz:220829_8merInsertion-Jurkat_Stimulation-Amp_PPIF_promoter-BioRep2-FFrep1-BinD-PCRrep2_I1"
],
"content_type": "reads",
"creation_timestamp": "2023-12-05T20:23:15.943875+00:00",
"file_format": "fastq",
"file_size": 3216940,
"href": "/sequence-files/IGVFFI8749BGVD/@@download/IGVFFI8749BGVD.fastq.gz",
"s3_uri": "s3://igvf-files/2023/12/05/838ae421-5868-4fad-ac32-18fba713b076/IGVFFI8749BGVD.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_S15-BioRep2-FFRep1-BinD-PCRrep2_S187_I1_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI2200CONX/",
"accession": "IGVFFI2200CONX",
"aliases": [
"jesse-engreitz:220829_8merInsertion-Jurkat_Stimulation-Amp_PPIF_promoter-BioRep2-FFrep1-BinD-PCRrep2_I2"
],
"content_type": "reads",
"creation_timestamp": "2023-12-05T20:31:36.353598+00:00",
"file_format": "fastq",
"file_size": 3251108,
"href": "/sequence-files/IGVFFI2200CONX/@@download/IGVFFI2200CONX.fastq.gz",
"s3_uri": "s3://igvf-files/2023/12/05/010a78f6-fc3b-4f36-8681-580e578645d8/IGVFFI2200CONX.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_S15-BioRep2-FFRep1-BinD-PCRrep2_S187_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": "2023-12-20T23:03:48.633132+00:00",
"samples": [
{
"@id": "/in-vitro-systems/IGVFSM4221WRQS/",
"@type": [
"InVitroSystem",
"Biosample",
"Sample",
"Item"
],
"accession": "IGVFSM4221WRQS",
"aliases": [
"jesse-engreitz:220829_8merInsertion-Jurkat_Stimulation-Amp_PPIF_promoter-BioRep2-FFrep1-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": "2023-12-05T19:33:18.204741+00:00",
"summary": "cas mediated mutagenesis (Variant FlowFISH) integrating a guide (sgRNA) library targeting sequence variants in a genomic locus",
"uuid": "99727558-a187-4e25-948d-5aaedde23246"
}