{
"@context": "/terms/",
"@id": "/measurement-sets/IGVFDS2964LIUB/",
"@type": [
"MeasurementSet",
"FileSet",
"Item"
],
"accession": "IGVFDS2964LIUB",
"aliases": [
"jesse-engreitz:220829_8merInsertion-Jurkat_NoStimulation-Amp_PPIF_promoter-BioRep1-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 [IGVFDS2964LIUB](/measurement-sets/IGVFDS2964LIUB/) has sequence file(s) [IGVFFI5686JIQV](/sequence-files/IGVFFI5686JIQV/), [IGVFFI1532LIBR](/sequence-files/IGVFFI1532LIBR/), [IGVFFI9935YBLY](/sequence-files/IGVFFI9935YBLY/), [IGVFFI8351GWHW](/sequence-files/IGVFFI8351GWHW/), [IGVFFI8521QEIA](/sequence-files/IGVFFI8521QEIA/), [IGVFFI0557GLUA](/sequence-files/IGVFFI0557GLUA/), [IGVFFI7107OTNC](/sequence-files/IGVFFI7107OTNC/), [IGVFFI7211QHUC](/sequence-files/IGVFFI7211QHUC/) 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/IGVFDS2964LIUB/"
},
{
"category": "missing sequence specification",
"detail": "Measurement set [IGVFDS2964LIUB](/measurement-sets/IGVFDS2964LIUB/) has sequence file(s): [IGVFFI5686JIQV](/sequence-files/IGVFFI5686JIQV/), [IGVFFI1532LIBR](/sequence-files/IGVFFI1532LIBR/), [IGVFFI9935YBLY](/sequence-files/IGVFFI9935YBLY/), [IGVFFI8351GWHW](/sequence-files/IGVFFI8351GWHW/), [IGVFFI8521QEIA](/sequence-files/IGVFFI8521QEIA/), [IGVFFI0557GLUA](/sequence-files/IGVFFI0557GLUA/), [IGVFFI7107OTNC](/sequence-files/IGVFFI7107OTNC/), [IGVFFI7211QHUC](/sequence-files/IGVFFI7211QHUC/) 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/IGVFDS2964LIUB/"
},
{
"category": "mismatched status",
"detail": "Released in vitro system [IGVFSM0782RZCF](/in-vitro-systems/IGVFSM0782RZCF/) 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/IGVFSM0782RZCF/"
}
],
"WARNING": [
{
"category": "missing auxiliary set",
"detail": "Measurement set [IGVFDS2964LIUB](/measurement-sets/IGVFDS2964LIUB/) 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/IGVFDS2964LIUB/"
},
{
"category": "missing targeted genes",
"detail": "Measurement set [IGVFDS2964LIUB](/measurement-sets/IGVFDS2964LIUB/) 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/IGVFDS2964LIUB/"
}
]
},
"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": "2023-12-01T00:02:52.252283+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/IGVFFI5686JIQV/",
"accession": "IGVFFI5686JIQV",
"aliases": [
"jesse-engreitz:220829_8merInsertion-Jurkat_NoStimulation-Amp_PPIF_promoter-BioRep1-FFrep1-FACS_Input-PCRrep2_I1"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2023-12-05T19:12:45.970861+00:00",
"file_format": "fastq",
"file_size": 2962771,
"href": "/sequence-files/IGVFFI5686JIQV/@@download/IGVFFI5686JIQV.fastq.gz",
"s3_uri": "s3://igvf-files/2023/12/05/2708e1ef-2a34-4ece-a59a-ecbf86d0769f/IGVFFI5686JIQV.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_S2-BioRep1-FFRep1-BinAll-PCRrep2_S63_I1_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI1532LIBR/",
"accession": "IGVFFI1532LIBR",
"aliases": [
"jesse-engreitz:220829_8merInsertion-Jurkat_NoStimulation-Amp_PPIF_promoter-BioRep1-FFrep1-FACS_Input-PCRrep2_R2"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2023-12-05T19:00:01.149322+00:00",
"file_format": "fastq",
"file_size": 12698598,
"href": "/sequence-files/IGVFFI1532LIBR/@@download/IGVFFI1532LIBR.fastq.gz",
"s3_uri": "s3://igvf-files/2023/12/05/7da2a8d4-3af0-4f43-bd96-c80679d29e44/IGVFFI1532LIBR.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_S2-BioRep1-FFRep1-BinAll-PCRrep2_S63_R2_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI9935YBLY/",
"accession": "IGVFFI9935YBLY",
"aliases": [
"jesse-engreitz:220829_8merInsertion-Jurkat_NoStimulation-Amp_PPIF_promoter-BioRep1-FFrep1-FACS_Input-PCRrep1_I1"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2023-12-05T19:06:32.348156+00:00",
"file_format": "fastq",
"file_size": 3435988,
"href": "/sequence-files/IGVFFI9935YBLY/@@download/IGVFFI9935YBLY.fastq.gz",
"s3_uri": "s3://igvf-files/2023/12/05/7124ff3c-3352-4cba-b5c4-fe3f01754051/IGVFFI9935YBLY.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_S2-BioRep1-FFRep1-BinAll-PCRrep1_S7_I1_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI8351GWHW/",
"accession": "IGVFFI8351GWHW",
"aliases": [
"jesse-engreitz:220829_8merInsertion-Jurkat_NoStimulation-Amp_PPIF_promoter-BioRep1-FFrep1-FACS_Input-PCRrep1_R1"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2023-12-05T18:40:46.164429+00:00",
"file_format": "fastq",
"file_size": 7884984,
"href": "/sequence-files/IGVFFI8351GWHW/@@download/IGVFFI8351GWHW.fastq.gz",
"s3_uri": "s3://igvf-files/2023/12/05/78c8c34c-f80a-4049-82a3-9d79954817cb/IGVFFI8351GWHW.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_S2-BioRep1-FFRep1-BinAll-PCRrep1_S7_R1_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI8521QEIA/",
"accession": "IGVFFI8521QEIA",
"aliases": [
"jesse-engreitz:220829_8merInsertion-Jurkat_NoStimulation-Amp_PPIF_promoter-BioRep1-FFrep1-FACS_Input-PCRrep1_R2"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2023-12-05T18:53:24.807793+00:00",
"file_format": "fastq",
"file_size": 14439926,
"href": "/sequence-files/IGVFFI8521QEIA/@@download/IGVFFI8521QEIA.fastq.gz",
"s3_uri": "s3://igvf-files/2023/12/05/b2414bfc-a6b1-4d1a-9002-63f6c106c651/IGVFFI8521QEIA.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_S2-BioRep1-FFRep1-BinAll-PCRrep1_S7_R2_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI0557GLUA/",
"accession": "IGVFFI0557GLUA",
"aliases": [
"jesse-engreitz:220829_8merInsertion-Jurkat_NoStimulation-Amp_PPIF_promoter-BioRep1-FFrep1-FACS_Input-PCRrep2_R1"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2023-12-05T18:47:04.542514+00:00",
"file_format": "fastq",
"file_size": 6934571,
"href": "/sequence-files/IGVFFI0557GLUA/@@download/IGVFFI0557GLUA.fastq.gz",
"s3_uri": "s3://igvf-files/2023/12/05/99f92aa2-a145-42e5-a10f-7412f3160e81/IGVFFI0557GLUA.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_S2-BioRep1-FFRep1-BinAll-PCRrep2_S63_R1_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI7107OTNC/",
"accession": "IGVFFI7107OTNC",
"aliases": [
"jesse-engreitz:220829_8merInsertion-Jurkat_NoStimulation-Amp_PPIF_promoter-BioRep1-FFrep1-FACS_Input-PCRrep1_I2"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2023-12-05T19:19:00.717240+00:00",
"file_format": "fastq",
"file_size": 3218853,
"href": "/sequence-files/IGVFFI7107OTNC/@@download/IGVFFI7107OTNC.fastq.gz",
"s3_uri": "s3://igvf-files/2023/12/05/3e8986f7-728a-48e0-90a3-f30eee4552e4/IGVFFI7107OTNC.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_S2-BioRep1-FFRep1-BinAll-PCRrep1_S7_I2_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI7211QHUC/",
"accession": "IGVFFI7211QHUC",
"aliases": [
"jesse-engreitz:220829_8merInsertion-Jurkat_NoStimulation-Amp_PPIF_promoter-BioRep1-FFrep1-FACS_Input-PCRrep2_I2"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2023-12-05T19:25:21.862339+00:00",
"file_format": "fastq",
"file_size": 2845924,
"href": "/sequence-files/IGVFFI7211QHUC/@@download/IGVFFI7211QHUC.fastq.gz",
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"sequencing_platform": {
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"status": "released",
"term_name": "Illumina NextSeq 550"
},
"status": "released",
"submitted_file_name": "220829_pPPIF_JurkatVFF-Jurkat-PE2A-BFP-pPPIF-Amp_pPPIF_S2-BioRep1-FFRep1-BinAll-PCRrep2_S63_I2_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": "2023-12-20T23:03:52.574487+00:00",
"samples": [
{
"@id": "/in-vitro-systems/IGVFSM0782RZCF/",
"@type": [
"InVitroSystem",
"Biosample",
"Sample",
"Item"
],
"accession": "IGVFSM0782RZCF",
"aliases": [
"jesse-engreitz:220829_8merInsertion-Jurkat_NoStimulation-Amp_PPIF_promoter-BioRep1-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": "2023-12-05T18:40:46.164429+00:00",
"summary": "unsorted FACS input CRISPR prime editing Variant-EFFECTS integrating a guide (sgRNA) library targeting sequence variants in a genomic locus",
"uuid": "a4a054eb-445c-42da-bdaf-2e1d6bd5e855"
}