{
"@context": "/terms/",
"@id": "/measurement-sets/IGVFDS2928NFHD/",
"@type": [
"MeasurementSet",
"FileSet",
"Item"
],
"accession": "IGVFDS2928NFHD",
"aliases": [
"jesse-engreitz:220829_8merInsertion-Jurkat_Stimulation-Amp_PPIF_promoter-BioRep2-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": "mismatched status",
"detail": "Released in vitro system [IGVFSM5748NPYI](/in-vitro-systems/IGVFSM5748NPYI/) 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/IGVFSM5748NPYI/"
},
{
"category": "missing sequencing kit",
"detail": "Measurement set [IGVFDS2928NFHD](/measurement-sets/IGVFDS2928NFHD/) has sequence file(s) [IGVFFI2149JOWE](/sequence-files/IGVFFI2149JOWE/), [IGVFFI7024FTBH](/sequence-files/IGVFFI7024FTBH/), [IGVFFI7993UJLK](/sequence-files/IGVFFI7993UJLK/), [IGVFFI7748QBQD](/sequence-files/IGVFFI7748QBQD/), [IGVFFI9190LNJB](/sequence-files/IGVFFI9190LNJB/), [IGVFFI2033IPXL](/sequence-files/IGVFFI2033IPXL/), [IGVFFI5019KMUJ](/sequence-files/IGVFFI5019KMUJ/), [IGVFFI5229CTAH](/sequence-files/IGVFFI5229CTAH/) 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/IGVFDS2928NFHD/"
},
{
"category": "missing sequence specification",
"detail": "Measurement set [IGVFDS2928NFHD](/measurement-sets/IGVFDS2928NFHD/) has sequence file(s): [IGVFFI2149JOWE](/sequence-files/IGVFFI2149JOWE/), [IGVFFI7024FTBH](/sequence-files/IGVFFI7024FTBH/), [IGVFFI7993UJLK](/sequence-files/IGVFFI7993UJLK/), [IGVFFI7748QBQD](/sequence-files/IGVFFI7748QBQD/), [IGVFFI9190LNJB](/sequence-files/IGVFFI9190LNJB/), [IGVFFI2033IPXL](/sequence-files/IGVFFI2033IPXL/), [IGVFFI5019KMUJ](/sequence-files/IGVFFI5019KMUJ/), [IGVFFI5229CTAH](/sequence-files/IGVFFI5229CTAH/) 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/IGVFDS2928NFHD/"
}
],
"WARNING": [
{
"category": "missing auxiliary set",
"detail": "Measurement set [IGVFDS2928NFHD](/measurement-sets/IGVFDS2928NFHD/) 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/IGVFDS2928NFHD/"
},
{
"category": "missing targeted genes",
"detail": "Measurement set [IGVFDS2928NFHD](/measurement-sets/IGVFDS2928NFHD/) 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/IGVFDS2928NFHD/"
}
]
},
"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": "2023-11-30T22:48:02.931881+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/IGVFFI2149JOWE/",
"accession": "IGVFFI2149JOWE",
"aliases": [
"jesse-engreitz:220829_8merInsertion-Jurkat_Stimulation-Amp_PPIF_promoter-BioRep2-FFrep1-FACS_Input-PCRrep2_R2"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2023-12-05T20:15:18.569333+00:00",
"file_format": "fastq",
"file_size": 15154767,
"href": "/sequence-files/IGVFFI2149JOWE/@@download/IGVFFI2149JOWE.fastq.gz",
"s3_uri": "s3://igvf-files/2023/12/05/dba9218c-d280-4ab3-addc-5f55d9f9dc52/IGVFFI2149JOWE.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_pPPIF2_S15-BioRep2-FFRep1-BinAll-PCRrep2_S190_R2_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI7024FTBH/",
"accession": "IGVFFI7024FTBH",
"aliases": [
"jesse-engreitz:220829_8merInsertion-Jurkat_Stimulation-Amp_PPIF_promoter-BioRep2-FFrep1-FACS_Input-PCRrep1_R1"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2023-12-05T19:33:45.222839+00:00",
"file_format": "fastq",
"file_size": 7812684,
"href": "/sequence-files/IGVFFI7024FTBH/@@download/IGVFFI7024FTBH.fastq.gz",
"s3_uri": "s3://igvf-files/2023/12/05/345deeb1-ab04-4ff4-94e2-2712e31a7743/IGVFFI7024FTBH.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_pPPIF2_S15-BioRep2-FFRep1-BinAll-PCRrep1_S133_R1_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI7993UJLK/",
"accession": "IGVFFI7993UJLK",
"aliases": [
"jesse-engreitz:220829_8merInsertion-Jurkat_Stimulation-Amp_PPIF_promoter-BioRep2-FFrep1-FACS_Input-PCRrep1_I2"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2023-12-05T19:58:44.565776+00:00",
"file_format": "fastq",
"file_size": 3264771,
"href": "/sequence-files/IGVFFI7993UJLK/@@download/IGVFFI7993UJLK.fastq.gz",
"s3_uri": "s3://igvf-files/2023/12/05/6378eeb7-543c-4227-ace1-449d96d17577/IGVFFI7993UJLK.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_pPPIF2_S15-BioRep2-FFRep1-BinAll-PCRrep1_S133_I2_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI7748QBQD/",
"accession": "IGVFFI7748QBQD",
"aliases": [
"jesse-engreitz:220829_8merInsertion-Jurkat_Stimulation-Amp_PPIF_promoter-BioRep2-FFrep1-FACS_Input-PCRrep2_R1"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2023-12-05T20:06:56.585627+00:00",
"file_format": "fastq",
"file_size": 8115805,
"href": "/sequence-files/IGVFFI7748QBQD/@@download/IGVFFI7748QBQD.fastq.gz",
"s3_uri": "s3://igvf-files/2023/12/05/7e0403f5-c2d7-4927-99e4-edc29b06d319/IGVFFI7748QBQD.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_pPPIF2_S15-BioRep2-FFRep1-BinAll-PCRrep2_S190_R1_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI9190LNJB/",
"accession": "IGVFFI9190LNJB",
"aliases": [
"jesse-engreitz:220829_8merInsertion-Jurkat_Stimulation-Amp_PPIF_promoter-BioRep2-FFrep1-FACS_Input-PCRrep2_I2"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2023-12-05T20:32:02.660483+00:00",
"file_format": "fastq",
"file_size": 3373519,
"href": "/sequence-files/IGVFFI9190LNJB/@@download/IGVFFI9190LNJB.fastq.gz",
"s3_uri": "s3://igvf-files/2023/12/05/cfda0d50-5d37-475a-b6bb-fc36938ef8bc/IGVFFI9190LNJB.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_pPPIF2_S15-BioRep2-FFRep1-BinAll-PCRrep2_S190_I2_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI2033IPXL/",
"accession": "IGVFFI2033IPXL",
"aliases": [
"jesse-engreitz:220829_8merInsertion-Jurkat_Stimulation-Amp_PPIF_promoter-BioRep2-FFrep1-FACS_Input-PCRrep1_I1"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2023-12-05T19:50:37.257508+00:00",
"file_format": "fastq",
"file_size": 3375672,
"href": "/sequence-files/IGVFFI2033IPXL/@@download/IGVFFI2033IPXL.fastq.gz",
"s3_uri": "s3://igvf-files/2023/12/05/4642b79f-9809-4197-aa82-99bb2128ac0b/IGVFFI2033IPXL.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_pPPIF2_S15-BioRep2-FFRep1-BinAll-PCRrep1_S133_I1_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI5019KMUJ/",
"accession": "IGVFFI5019KMUJ",
"aliases": [
"jesse-engreitz:220829_8merInsertion-Jurkat_Stimulation-Amp_PPIF_promoter-BioRep2-FFrep1-FACS_Input-PCRrep1_R2"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2023-12-05T19:42:07.721743+00:00",
"file_format": "fastq",
"file_size": 14532740,
"href": "/sequence-files/IGVFFI5019KMUJ/@@download/IGVFFI5019KMUJ.fastq.gz",
"s3_uri": "s3://igvf-files/2023/12/05/3b708415-0cba-4b62-9919-c3b64ec160fe/IGVFFI5019KMUJ.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_pPPIF2_S15-BioRep2-FFRep1-BinAll-PCRrep1_S133_R2_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI5229CTAH/",
"accession": "IGVFFI5229CTAH",
"aliases": [
"jesse-engreitz:220829_8merInsertion-Jurkat_Stimulation-Amp_PPIF_promoter-BioRep2-FFrep1-FACS_Input-PCRrep2_I1"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2023-12-05T20:23:42.125548+00:00",
"file_format": "fastq",
"file_size": 3750250,
"href": "/sequence-files/IGVFFI5229CTAH/@@download/IGVFFI5229CTAH.fastq.gz",
"s3_uri": "s3://igvf-files/2023/12/05/b3404c2d-f426-45fc-bb48-edad3abf5ad2/IGVFFI5229CTAH.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_pPPIF2_S15-BioRep2-FFRep1-BinAll-PCRrep2_S190_I1_001.fastq.gz",
"upload_status": "validated"
}
],
"input_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. 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": "2023-12-20T23:04:29.503857+00:00",
"samples": [
{
"@id": "/in-vitro-systems/IGVFSM5748NPYI/",
"@type": [
"InVitroSystem",
"Biosample",
"Sample",
"Item"
],
"accession": "IGVFSM5748NPYI",
"aliases": [
"jesse-engreitz:220829_8merInsertion-Jurkat_Stimulation-Amp_PPIF_promoter-BioRep2-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 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 CRISPR prime editing Sp-nCas9-M-MLV RT (PE2), transfected with a guide library",
"taxa": "Homo sapiens",
"treatments": [
{
"@id": "/treatments/df02c0d4-f796-4f77-bfbc-388cdbfcc615/",
"status": "released",
"treatment_term_name": "T-cell surface glycoprotein CD3 gamma chain"
},
{
"@id": "/treatments/42b3c61d-38de-4bd2-bb39-33c125a417cb/",
"status": "released",
"treatment_term_name": "phorbol 13-acetate 12-myristate"
}
]
}
],
"schema_version": "23",
"status": "released",
"submitted_by": {
"@id": "/users/f9e7cd82-a407-4a20-89ee-f4dc668b0cbe/",
"title": "Michael Montgomery"
},
"submitted_files_timestamp": "2023-12-05T19:33:45.222839+00:00",
"summary": "unsorted FACS input CRISPR prime editing Variant-EFFECTS integrating a guide (sgRNA) library targeting sequence variants in a genomic locus",
"uuid": "292c1bda-b84c-4063-9900-d22ba248ae26"
}