{
"@context": "/terms/",
"@id": "/measurement-sets/IGVFDS6978TYGN/",
"@type": [
"MeasurementSet",
"FileSet",
"Item"
],
"accession": "IGVFDS6978TYGN",
"aliases": [
"jesse-engreitz:220829_8merInsertion-Jurkat_NoStimulation-Amp_PPIF_promoter-BioRep1-FFrep2-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": "mismatched status",
"detail": "Released in vitro system [IGVFSM1472HFYH](/in-vitro-systems/IGVFSM1472HFYH/) 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/IGVFSM1472HFYH/"
},
{
"category": "missing sequencing kit",
"detail": "Measurement set [IGVFDS6978TYGN](/measurement-sets/IGVFDS6978TYGN/) has sequence file(s) [IGVFFI0975EZFH](/sequence-files/IGVFFI0975EZFH/), [IGVFFI5381BVQF](/sequence-files/IGVFFI5381BVQF/), [IGVFFI8575RPUV](/sequence-files/IGVFFI8575RPUV/), [IGVFFI8561HSFP](/sequence-files/IGVFFI8561HSFP/), [IGVFFI8133ZKWG](/sequence-files/IGVFFI8133ZKWG/), [IGVFFI2187CIEU](/sequence-files/IGVFFI2187CIEU/), [IGVFFI2538PSMK](/sequence-files/IGVFFI2538PSMK/), [IGVFFI3077XAHB](/sequence-files/IGVFFI3077XAHB/) 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/IGVFDS6978TYGN/"
},
{
"category": "missing sequence specification",
"detail": "Measurement set [IGVFDS6978TYGN](/measurement-sets/IGVFDS6978TYGN/) has sequence file(s): [IGVFFI0975EZFH](/sequence-files/IGVFFI0975EZFH/), [IGVFFI5381BVQF](/sequence-files/IGVFFI5381BVQF/), [IGVFFI8575RPUV](/sequence-files/IGVFFI8575RPUV/), [IGVFFI8561HSFP](/sequence-files/IGVFFI8561HSFP/), [IGVFFI8133ZKWG](/sequence-files/IGVFFI8133ZKWG/), [IGVFFI2187CIEU](/sequence-files/IGVFFI2187CIEU/), [IGVFFI2538PSMK](/sequence-files/IGVFFI2538PSMK/), [IGVFFI3077XAHB](/sequence-files/IGVFFI3077XAHB/) 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/IGVFDS6978TYGN/"
}
],
"WARNING": [
{
"category": "missing auxiliary set",
"detail": "Measurement set [IGVFDS6978TYGN](/measurement-sets/IGVFDS6978TYGN/) 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/IGVFDS6978TYGN/"
},
{
"category": "missing targeted genes",
"detail": "Measurement set [IGVFDS6978TYGN](/measurement-sets/IGVFDS6978TYGN/) 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/IGVFDS6978TYGN/"
}
]
},
"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": "2023-11-30T22:47:09.056029+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/IGVFFI0975EZFH/",
"accession": "IGVFFI0975EZFH",
"aliases": [
"jesse-engreitz:220829_8merInsertion-Jurkat_NoStimulation-Amp_PPIF_promoter-BioRep1-FFrep2-FACS_Input-PCRrep2_I2"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2023-12-05T19:26:23.280368+00:00",
"file_format": "fastq",
"file_size": 3262860,
"href": "/sequence-files/IGVFFI0975EZFH/@@download/IGVFFI0975EZFH.fastq.gz",
"s3_uri": "s3://igvf-files/2023/12/05/a5b75d39-e15a-4edc-a152-23347bdb810e/IGVFFI0975EZFH.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_S3-BioRep1-FFRep2-BinAll-PCRrep2_S70_I2_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI5381BVQF/",
"accession": "IGVFFI5381BVQF",
"aliases": [
"jesse-engreitz:220829_8merInsertion-Jurkat_NoStimulation-Amp_PPIF_promoter-BioRep1-FFrep2-FACS_Input-PCRrep1_I2"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2023-12-05T19:20:02.342905+00:00",
"file_format": "fastq",
"file_size": 3084492,
"href": "/sequence-files/IGVFFI5381BVQF/@@download/IGVFFI5381BVQF.fastq.gz",
"s3_uri": "s3://igvf-files/2023/12/05/0fb98beb-a771-40ed-8cef-b4f4c21d2809/IGVFFI5381BVQF.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_S3-BioRep1-FFRep2-BinAll-PCRrep1_S14_I2_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI8575RPUV/",
"accession": "IGVFFI8575RPUV",
"aliases": [
"jesse-engreitz:220829_8merInsertion-Jurkat_NoStimulation-Amp_PPIF_promoter-BioRep1-FFrep2-FACS_Input-PCRrep2_I1"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2023-12-05T19:13:47.092357+00:00",
"file_format": "fastq",
"file_size": 3545779,
"href": "/sequence-files/IGVFFI8575RPUV/@@download/IGVFFI8575RPUV.fastq.gz",
"s3_uri": "s3://igvf-files/2023/12/05/fcb4f183-27cb-45c8-bc2c-032e878c0c22/IGVFFI8575RPUV.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_S3-BioRep1-FFRep2-BinAll-PCRrep2_S70_I1_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI8561HSFP/",
"accession": "IGVFFI8561HSFP",
"aliases": [
"jesse-engreitz:220829_8merInsertion-Jurkat_NoStimulation-Amp_PPIF_promoter-BioRep1-FFrep2-FACS_Input-PCRrep1_R1"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2023-12-05T18:41:47.739021+00:00",
"file_format": "fastq",
"file_size": 7499843,
"href": "/sequence-files/IGVFFI8561HSFP/@@download/IGVFFI8561HSFP.fastq.gz",
"s3_uri": "s3://igvf-files/2023/12/05/aa7bf62e-8b5b-4d98-873b-8c65fe7f96a4/IGVFFI8561HSFP.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_S3-BioRep1-FFRep2-BinAll-PCRrep1_S14_R1_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI8133ZKWG/",
"accession": "IGVFFI8133ZKWG",
"aliases": [
"jesse-engreitz:220829_8merInsertion-Jurkat_NoStimulation-Amp_PPIF_promoter-BioRep1-FFrep2-FACS_Input-PCRrep2_R1"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2023-12-05T18:48:06.202419+00:00",
"file_format": "fastq",
"file_size": 7944261,
"href": "/sequence-files/IGVFFI8133ZKWG/@@download/IGVFFI8133ZKWG.fastq.gz",
"s3_uri": "s3://igvf-files/2023/12/05/7773e1fe-957c-4900-9646-b724dc04d6a7/IGVFFI8133ZKWG.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_S3-BioRep1-FFRep2-BinAll-PCRrep2_S70_R1_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI2187CIEU/",
"accession": "IGVFFI2187CIEU",
"aliases": [
"jesse-engreitz:220829_8merInsertion-Jurkat_NoStimulation-Amp_PPIF_promoter-BioRep1-FFrep2-FACS_Input-PCRrep1_R2"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2023-12-05T18:54:28.851528+00:00",
"file_format": "fastq",
"file_size": 13745822,
"href": "/sequence-files/IGVFFI2187CIEU/@@download/IGVFFI2187CIEU.fastq.gz",
"s3_uri": "s3://igvf-files/2023/12/05/8b0cdba5-4095-444c-bbf4-06fd45df5d28/IGVFFI2187CIEU.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_S3-BioRep1-FFRep2-BinAll-PCRrep1_S14_R2_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI2538PSMK/",
"accession": "IGVFFI2538PSMK",
"aliases": [
"jesse-engreitz:220829_8merInsertion-Jurkat_NoStimulation-Amp_PPIF_promoter-BioRep1-FFrep2-FACS_Input-PCRrep1_I1"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2023-12-05T19:07:32.389201+00:00",
"file_format": "fastq",
"file_size": 3135966,
"href": "/sequence-files/IGVFFI2538PSMK/@@download/IGVFFI2538PSMK.fastq.gz",
"s3_uri": "s3://igvf-files/2023/12/05/6f0e358b-4cad-4abb-aacb-d788747794ca/IGVFFI2538PSMK.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_S3-BioRep1-FFRep2-BinAll-PCRrep1_S14_I1_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI3077XAHB/",
"accession": "IGVFFI3077XAHB",
"aliases": [
"jesse-engreitz:220829_8merInsertion-Jurkat_NoStimulation-Amp_PPIF_promoter-BioRep1-FFrep2-FACS_Input-PCRrep2_R2"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2023-12-05T19:01:06.177897+00:00",
"file_format": "fastq",
"file_size": 14559911,
"href": "/sequence-files/IGVFFI3077XAHB/@@download/IGVFFI3077XAHB.fastq.gz",
"s3_uri": "s3://igvf-files/2023/12/05/9f1f48fe-bca0-441f-9b95-275a3632bfe1/IGVFFI3077XAHB.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_S3-BioRep1-FFRep2-BinAll-PCRrep2_S70_R2_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": "2023-12-20T23:04:00.112068+00:00",
"samples": [
{
"@id": "/in-vitro-systems/IGVFSM1472HFYH/",
"@type": [
"InVitroSystem",
"Biosample",
"Sample",
"Item"
],
"accession": "IGVFSM1472HFYH",
"aliases": [
"jesse-engreitz:220829_8merInsertion-Jurkat_NoStimulation-Amp_PPIF_promoter-BioRep1-FFrep2-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": "2023-12-05T18:41:47.739021+00:00",
"summary": "unsorted FACS input CRISPR prime editing Variant-EFFECTS integrating a guide (sgRNA) library targeting sequence variants in a genomic locus",
"uuid": "10f5210f-3175-4f34-b74a-691d654ca94a"
}