{
"@context": "/terms/",
"@id": "/measurement-sets/IGVFDS0596BXTA/",
"@type": [
"MeasurementSet",
"FileSet",
"Item"
],
"accession": "IGVFDS0596BXTA",
"aliases": [
"jesse-engreitz:220829_8merInsertion-Jurkat_NoStimulation-Amp_PPIF_promoter-BioRep3-FFrep1-FACS_Input_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 [IGVFDS0596BXTA](/measurement-sets/IGVFDS0596BXTA/) has sequence file(s) [IGVFFI4628JPPL](/sequence-files/IGVFFI4628JPPL/), [IGVFFI6627IMTF](/sequence-files/IGVFFI6627IMTF/), [IGVFFI8360NICR](/sequence-files/IGVFFI8360NICR/), [IGVFFI1041CZZY](/sequence-files/IGVFFI1041CZZY/), [IGVFFI7367VCPG](/sequence-files/IGVFFI7367VCPG/), [IGVFFI4216OQFJ](/sequence-files/IGVFFI4216OQFJ/), [IGVFFI9210TSHW](/sequence-files/IGVFFI9210TSHW/), [IGVFFI5585NHCS](/sequence-files/IGVFFI5585NHCS/) 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/IGVFDS0596BXTA/"
},
{
"category": "missing sequence specification",
"detail": "Measurement set [IGVFDS0596BXTA](/measurement-sets/IGVFDS0596BXTA/) has sequence file(s): [IGVFFI4628JPPL](/sequence-files/IGVFFI4628JPPL/), [IGVFFI6627IMTF](/sequence-files/IGVFFI6627IMTF/), [IGVFFI8360NICR](/sequence-files/IGVFFI8360NICR/), [IGVFFI1041CZZY](/sequence-files/IGVFFI1041CZZY/), [IGVFFI7367VCPG](/sequence-files/IGVFFI7367VCPG/), [IGVFFI4216OQFJ](/sequence-files/IGVFFI4216OQFJ/), [IGVFFI9210TSHW](/sequence-files/IGVFFI9210TSHW/), [IGVFFI5585NHCS](/sequence-files/IGVFFI5585NHCS/) 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/IGVFDS0596BXTA/"
},
{
"category": "mismatched status",
"detail": "Released in vitro system [IGVFSM6234QUUU](/in-vitro-systems/IGVFSM6234QUUU/) 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/IGVFSM6234QUUU/"
}
],
"WARNING": [
{
"category": "missing auxiliary set",
"detail": "Measurement set [IGVFDS0596BXTA](/measurement-sets/IGVFDS0596BXTA/) 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/IGVFDS0596BXTA/"
},
{
"category": "missing targeted genes",
"detail": "Measurement set [IGVFDS0596BXTA](/measurement-sets/IGVFDS0596BXTA/) has no `targeted_genes`. ChIP-seq and CRISPR flow cytometry assays are expected to specify targeted gene(s).",
"level": 40,
"level_name": "WARNING",
"name": "audit_targeted_genes",
"path": "/measurement-sets/IGVFDS0596BXTA/"
}
]
},
"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": [],
"control_type": "unsorted FACS input",
"creation_timestamp": "2023-11-30T22:47:31.258029+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/IGVFFI4628JPPL/",
"accession": "IGVFFI4628JPPL",
"aliases": [
"jesse-engreitz:220829_8merInsertion-Jurkat_NoStimulation-Amp_PPIF_promoter-BioRep3-FFrep1-FACS_Input-PCRrep2_I2"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2023-12-05T19:29:25.549146+00:00",
"file_format": "fastq",
"file_size": 3251615,
"href": "/sequence-files/IGVFFI4628JPPL/@@download/IGVFFI4628JPPL.fastq.gz",
"s3_uri": "s3://igvf-files/2023/12/05/e8a59320-c899-4a2d-bb92-67433af26bfc/IGVFFI4628JPPL.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_pPPIF_S7-BioRep3-FFRep1-BinAll-PCRrep2_S91_I2_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI6627IMTF/",
"accession": "IGVFFI6627IMTF",
"aliases": [
"jesse-engreitz:220829_8merInsertion-Jurkat_NoStimulation-Amp_PPIF_promoter-BioRep3-FFrep1-FACS_Input-PCRrep1_R1"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2023-12-05T18:44:51.590169+00:00",
"file_format": "fastq",
"file_size": 7982313,
"href": "/sequence-files/IGVFFI6627IMTF/@@download/IGVFFI6627IMTF.fastq.gz",
"s3_uri": "s3://igvf-files/2023/12/05/398ed1af-a72d-4c1e-b4e5-e6d0a4a7db13/IGVFFI6627IMTF.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_pPPIF_S7-BioRep3-FFRep1-BinAll-PCRrep1_S35_R1_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI8360NICR/",
"accession": "IGVFFI8360NICR",
"aliases": [
"jesse-engreitz:220829_8merInsertion-Jurkat_NoStimulation-Amp_PPIF_promoter-BioRep3-FFrep1-FACS_Input-PCRrep1_I1"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2023-12-05T19:10:34.858553+00:00",
"file_format": "fastq",
"file_size": 3476728,
"href": "/sequence-files/IGVFFI8360NICR/@@download/IGVFFI8360NICR.fastq.gz",
"s3_uri": "s3://igvf-files/2023/12/05/b8498faa-0721-4272-a9d7-d8e5bd313627/IGVFFI8360NICR.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_pPPIF_S7-BioRep3-FFRep1-BinAll-PCRrep1_S35_I1_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI1041CZZY/",
"accession": "IGVFFI1041CZZY",
"aliases": [
"jesse-engreitz:220829_8merInsertion-Jurkat_NoStimulation-Amp_PPIF_promoter-BioRep3-FFrep1-FACS_Input-PCRrep1_I2"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2023-12-05T19:23:10.833817+00:00",
"file_format": "fastq",
"file_size": 3268500,
"href": "/sequence-files/IGVFFI1041CZZY/@@download/IGVFFI1041CZZY.fastq.gz",
"s3_uri": "s3://igvf-files/2023/12/05/b53a869d-a0c7-4878-889d-e709e2113571/IGVFFI1041CZZY.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_pPPIF_S7-BioRep3-FFRep1-BinAll-PCRrep1_S35_I2_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI7367VCPG/",
"accession": "IGVFFI7367VCPG",
"aliases": [
"jesse-engreitz:220829_8merInsertion-Jurkat_NoStimulation-Amp_PPIF_promoter-BioRep3-FFrep1-FACS_Input-PCRrep1_R2"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2023-12-05T18:57:40.416912+00:00",
"file_format": "fastq",
"file_size": 14668251,
"href": "/sequence-files/IGVFFI7367VCPG/@@download/IGVFFI7367VCPG.fastq.gz",
"s3_uri": "s3://igvf-files/2023/12/05/7d9f8f5d-893b-441b-86c7-2a0be9930d3c/IGVFFI7367VCPG.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_pPPIF_S7-BioRep3-FFRep1-BinAll-PCRrep1_S35_R2_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI4216OQFJ/",
"accession": "IGVFFI4216OQFJ",
"aliases": [
"jesse-engreitz:220829_8merInsertion-Jurkat_NoStimulation-Amp_PPIF_promoter-BioRep3-FFrep1-FACS_Input-PCRrep2_R2"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2023-12-05T19:04:17.727845+00:00",
"file_format": "fastq",
"file_size": 14506970,
"href": "/sequence-files/IGVFFI4216OQFJ/@@download/IGVFFI4216OQFJ.fastq.gz",
"s3_uri": "s3://igvf-files/2023/12/05/ad134e19-3cdf-4898-8f33-4e1e3987f1b5/IGVFFI4216OQFJ.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_pPPIF_S7-BioRep3-FFRep1-BinAll-PCRrep2_S91_R2_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI9210TSHW/",
"accession": "IGVFFI9210TSHW",
"aliases": [
"jesse-engreitz:220829_8merInsertion-Jurkat_NoStimulation-Amp_PPIF_promoter-BioRep3-FFrep1-FACS_Input-PCRrep2_R1"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2023-12-05T18:51:10.706162+00:00",
"file_format": "fastq",
"file_size": 7945398,
"href": "/sequence-files/IGVFFI9210TSHW/@@download/IGVFFI9210TSHW.fastq.gz",
"s3_uri": "s3://igvf-files/2023/12/05/f643dd03-918d-4dd5-8dcf-177ce094e54e/IGVFFI9210TSHW.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_pPPIF_S7-BioRep3-FFRep1-BinAll-PCRrep2_S91_R1_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI5585NHCS/",
"accession": "IGVFFI5585NHCS",
"aliases": [
"jesse-engreitz:220829_8merInsertion-Jurkat_NoStimulation-Amp_PPIF_promoter-BioRep3-FFrep1-FACS_Input-PCRrep2_I1"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2023-12-05T19:16:50.200216+00:00",
"file_format": "fastq",
"file_size": 3365342,
"href": "/sequence-files/IGVFFI5585NHCS/@@download/IGVFFI5585NHCS.fastq.gz",
"s3_uri": "s3://igvf-files/2023/12/05/6b66f655-be62-4c10-848c-69b51d24ec66/IGVFFI5585NHCS.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_pPPIF_S7-BioRep3-FFRep1-BinAll-PCRrep2_S91_I1_001.fastq.gz",
"upload_status": "validated"
}
],
"input_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. 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": "2023-12-20T23:10:38.401199+00:00",
"samples": [
{
"@id": "/in-vitro-systems/IGVFSM6234QUUU/",
"@type": [
"InVitroSystem",
"Biosample",
"Sample",
"Item"
],
"accession": "IGVFSM6234QUUU",
"aliases": [
"jesse-engreitz:220829_8merInsertion-Jurkat_NoStimulation-Amp_PPIF_promoter-BioRep3-FFrep1-FACS_Input"
],
"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 modified with CRISPR prime editing Sp-nCas9-M-MLV RT (PE2), transfected with a guide library",
"taxa": "Homo sapiens"
}
],
"schema_version": "23",
"status": "released",
"submitted_by": {
"@id": "/users/f9e7cd82-a407-4a20-89ee-f4dc668b0cbe/",
"title": "Michael Montgomery"
},
"submitted_files_timestamp": "2023-12-05T18:44:51.590169+00:00",
"summary": "unsorted FACS input CRISPR prime editing Variant-EFFECTS integrating a guide (sgRNA) library targeting sequence variants in a genomic locus",
"uuid": "8e0f1940-b4a6-4d55-bf4a-5c1831768af2"
}