{
"@context": "/terms/",
"@id": "/measurement-sets/IGVFDS6647HVMC/",
"@type": [
"MeasurementSet",
"FileSet",
"Item"
],
"accession": "IGVFDS6647HVMC",
"aliases": [
"jesse-engreitz:220829_8merInsertion-Jurkat_NoStimulation-Amp_PPIF_promoter-BioRep3-FFrep1-BinB_AmpliconSequencing"
],
"assay_term": {
"@id": "/assay-terms/OBI_0003133/",
"term_name": "cas mediated mutagenesis"
},
"audit": {
"INTERNAL_ACTION": [
{
"category": "mismatched status",
"detail": "Released in vitro system [IGVFSM8601WYGY](/in-vitro-systems/IGVFSM8601WYGY/) 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/IGVFSM8601WYGY/"
}
],
"NOT_COMPLIANT": [
{
"category": "missing sequence specification",
"detail": "Measurement set [IGVFDS6647HVMC](/measurement-sets/IGVFDS6647HVMC/) has sequence file(s): [IGVFFI1297OKBA](/sequence-files/IGVFFI1297OKBA/), [IGVFFI3724EHBW](/sequence-files/IGVFFI3724EHBW/), [IGVFFI3823QCOY](/sequence-files/IGVFFI3823QCOY/), [IGVFFI7167LWVZ](/sequence-files/IGVFFI7167LWVZ/), [IGVFFI7777XMXM](/sequence-files/IGVFFI7777XMXM/), [IGVFFI5602OVOR](/sequence-files/IGVFFI5602OVOR/), [IGVFFI2917GROT](/sequence-files/IGVFFI2917GROT/), [IGVFFI9638BNPL](/sequence-files/IGVFFI9638BNPL/) 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/IGVFDS6647HVMC/"
},
{
"category": "missing auxiliary set",
"detail": "Measurement set [IGVFDS6647HVMC](/measurement-sets/IGVFDS6647HVMC/) 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/IGVFDS6647HVMC/"
},
{
"category": "missing auxiliary set",
"detail": "Measurement set [IGVFDS6647HVMC](/measurement-sets/IGVFDS6647HVMC/) 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/IGVFDS6647HVMC/"
},
{
"category": "missing targeted genes",
"detail": "Measurement set [IGVFDS6647HVMC](/measurement-sets/IGVFDS6647HVMC/) 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/IGVFDS6647HVMC/"
}
],
"WARNING": [
{
"category": "missing sequencing kit",
"detail": "Measurement set [IGVFDS6647HVMC](/measurement-sets/IGVFDS6647HVMC/) has sequence file(s) [IGVFFI1297OKBA](/sequence-files/IGVFFI1297OKBA/), [IGVFFI3724EHBW](/sequence-files/IGVFFI3724EHBW/), [IGVFFI3823QCOY](/sequence-files/IGVFFI3823QCOY/), [IGVFFI7167LWVZ](/sequence-files/IGVFFI7167LWVZ/), [IGVFFI7777XMXM](/sequence-files/IGVFFI7777XMXM/), [IGVFFI5602OVOR](/sequence-files/IGVFFI5602OVOR/), [IGVFFI2917GROT](/sequence-files/IGVFFI2917GROT/), [IGVFFI9638BNPL](/sequence-files/IGVFFI9638BNPL/) 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/IGVFDS6647HVMC/"
}
]
},
"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": "2023-11-30T22:47:32.147601+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/IGVFFI1297OKBA/",
"accession": "IGVFFI1297OKBA",
"aliases": [
"jesse-engreitz:220829_8merInsertion-Jurkat_NoStimulation-Amp_PPIF_promoter-BioRep3-FFrep1-BinB-PCRrep1_R1"
],
"content_type": "reads",
"creation_timestamp": "2023-12-05T18:44:07.994544+00:00",
"file_format": "fastq",
"file_size": 7231750,
"href": "/sequence-files/IGVFFI1297OKBA/@@download/IGVFFI1297OKBA.fastq.gz",
"s3_uri": "s3://igvf-files/2023/12/05/c7113a6b-f352-4a89-a455-1b4794f7f90c/IGVFFI1297OKBA.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_pPPIF_S7-BioRep3-FFRep1-BinB-PCRrep1_S30_R1_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI3724EHBW/",
"accession": "IGVFFI3724EHBW",
"aliases": [
"jesse-engreitz:220829_8merInsertion-Jurkat_NoStimulation-Amp_PPIF_promoter-BioRep3-FFrep1-BinB-PCRrep2_R1"
],
"content_type": "reads",
"creation_timestamp": "2023-12-05T18:50:26.809417+00:00",
"file_format": "fastq",
"file_size": 7922851,
"href": "/sequence-files/IGVFFI3724EHBW/@@download/IGVFFI3724EHBW.fastq.gz",
"s3_uri": "s3://igvf-files/2023/12/05/c78517e0-377d-4884-b391-37e1b0d3ca56/IGVFFI3724EHBW.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_pPPIF_S7-BioRep3-FFRep1-BinB-PCRrep2_S86_R1_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI3823QCOY/",
"accession": "IGVFFI3823QCOY",
"aliases": [
"jesse-engreitz:220829_8merInsertion-Jurkat_NoStimulation-Amp_PPIF_promoter-BioRep3-FFrep1-BinB-PCRrep2_R2"
],
"content_type": "reads",
"creation_timestamp": "2023-12-05T19:03:32.091399+00:00",
"file_format": "fastq",
"file_size": 14421299,
"href": "/sequence-files/IGVFFI3823QCOY/@@download/IGVFFI3823QCOY.fastq.gz",
"s3_uri": "s3://igvf-files/2023/12/05/cc3cfe4e-37e9-46fd-96a5-6667518c8774/IGVFFI3823QCOY.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_pPPIF_S7-BioRep3-FFRep1-BinB-PCRrep2_S86_R2_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI7167LWVZ/",
"accession": "IGVFFI7167LWVZ",
"aliases": [
"jesse-engreitz:220829_8merInsertion-Jurkat_NoStimulation-Amp_PPIF_promoter-BioRep3-FFrep1-BinB-PCRrep1_R2"
],
"content_type": "reads",
"creation_timestamp": "2023-12-05T18:56:54.968677+00:00",
"file_format": "fastq",
"file_size": 13119631,
"href": "/sequence-files/IGVFFI7167LWVZ/@@download/IGVFFI7167LWVZ.fastq.gz",
"s3_uri": "s3://igvf-files/2023/12/05/9bdcff2e-b0d7-41b5-a0e9-a9567361cb5e/IGVFFI7167LWVZ.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_pPPIF_S7-BioRep3-FFRep1-BinB-PCRrep1_S30_R2_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI7777XMXM/",
"accession": "IGVFFI7777XMXM",
"aliases": [
"jesse-engreitz:220829_8merInsertion-Jurkat_NoStimulation-Amp_PPIF_promoter-BioRep3-FFrep1-BinB-PCRrep1_I1"
],
"content_type": "reads",
"creation_timestamp": "2023-12-05T19:09:51.244876+00:00",
"file_format": "fastq",
"file_size": 3023678,
"href": "/sequence-files/IGVFFI7777XMXM/@@download/IGVFFI7777XMXM.fastq.gz",
"s3_uri": "s3://igvf-files/2023/12/05/32f8b441-ee6c-4739-a77b-4a77e431427b/IGVFFI7777XMXM.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_pPPIF_S7-BioRep3-FFRep1-BinB-PCRrep1_S30_I1_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI5602OVOR/",
"accession": "IGVFFI5602OVOR",
"aliases": [
"jesse-engreitz:220829_8merInsertion-Jurkat_NoStimulation-Amp_PPIF_promoter-BioRep3-FFrep1-BinB-PCRrep2_I1"
],
"content_type": "reads",
"creation_timestamp": "2023-12-05T19:16:06.766451+00:00",
"file_format": "fastq",
"file_size": 3488285,
"href": "/sequence-files/IGVFFI5602OVOR/@@download/IGVFFI5602OVOR.fastq.gz",
"s3_uri": "s3://igvf-files/2023/12/05/8bf99a2f-3943-4aa9-b46c-dd3354283f98/IGVFFI5602OVOR.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_pPPIF_S7-BioRep3-FFRep1-BinB-PCRrep2_S86_I1_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI2917GROT/",
"accession": "IGVFFI2917GROT",
"aliases": [
"jesse-engreitz:220829_8merInsertion-Jurkat_NoStimulation-Amp_PPIF_promoter-BioRep3-FFrep1-BinB-PCRrep1_I2"
],
"content_type": "reads",
"creation_timestamp": "2023-12-05T19:22:23.667058+00:00",
"file_format": "fastq",
"file_size": 2939965,
"href": "/sequence-files/IGVFFI2917GROT/@@download/IGVFFI2917GROT.fastq.gz",
"s3_uri": "s3://igvf-files/2023/12/05/a20926a0-f84b-4b07-b558-256013c5c24e/IGVFFI2917GROT.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_pPPIF_S7-BioRep3-FFRep1-BinB-PCRrep1_S30_I2_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI9638BNPL/",
"accession": "IGVFFI9638BNPL",
"aliases": [
"jesse-engreitz:220829_8merInsertion-Jurkat_NoStimulation-Amp_PPIF_promoter-BioRep3-FFrep1-BinB-PCRrep2_I2"
],
"content_type": "reads",
"creation_timestamp": "2023-12-05T19:28:42.250780+00:00",
"file_format": "fastq",
"file_size": 3235597,
"href": "/sequence-files/IGVFFI9638BNPL/@@download/IGVFFI9638BNPL.fastq.gz",
"s3_uri": "s3://igvf-files/2023/12/05/28ff8b79-ff2b-451e-af70-f6f9894b8236/IGVFFI9638BNPL.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_pPPIF_S7-BioRep3-FFRep1-BinB-PCRrep2_S86_I2_001.fastq.gz",
"upload_status": "validated"
}
],
"input_file_set_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.",
"preferred_assay_title": "Variant FlowFISH",
"protocols": [
"https://www.protocols.io/view/flowfish-with-primeflow-36wgq3q4olk5/v1"
],
"release_timestamp": "2023-12-20T23:04:37.145369+00:00",
"samples": [
{
"@id": "/in-vitro-systems/IGVFSM8601WYGY/",
"@type": [
"InVitroSystem",
"Biosample",
"Sample",
"Item"
],
"accession": "IGVFSM8601WYGY",
"aliases": [
"jesse-engreitz:220829_8merInsertion-Jurkat_NoStimulation-Amp_PPIF_promoter-BioRep3-FFrep1-BinB"
],
"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 11-20% expression of PPIF) modified with a guide library",
"taxa": "Homo sapiens"
}
],
"schema_version": "17",
"status": "released",
"submitted_by": {
"@id": "/users/f9e7cd82-a407-4a20-89ee-f4dc668b0cbe/",
"title": "Michael Montgomery"
},
"submitted_files_timestamp": "2023-12-05T18:44:07.994544+00:00",
"summary": "cas mediated mutagenesis (Variant FlowFISH) integrating a guide (sgRNA) library targeting sequence variants in a genomic locus",
"uuid": "feb7d08a-1287-4cac-b362-f81fd5ba1f81"
}