{
"@context": "/terms/",
"@id": "/measurement-sets/IGVFDS4869FXYY/",
"@type": [
"MeasurementSet",
"FileSet",
"Item"
],
"accession": "IGVFDS4869FXYY",
"aliases": [
"jesse-engreitz:230423pPPIFEnformer-Jurkat-Amp_PPIF_promoter-Jurkat-PE2_Exp2_NegControl_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 [IGVFDS4869FXYY](/measurement-sets/IGVFDS4869FXYY/) has sequence file(s) [IGVFFI4309IHNT](/sequence-files/IGVFFI4309IHNT/), [IGVFFI2033NCGX](/sequence-files/IGVFFI2033NCGX/), [IGVFFI3960PNJX](/sequence-files/IGVFFI3960PNJX/), [IGVFFI4195XTAZ](/sequence-files/IGVFFI4195XTAZ/), [IGVFFI6572WWXH](/sequence-files/IGVFFI6572WWXH/), [IGVFFI3167OFUE](/sequence-files/IGVFFI3167OFUE/), [IGVFFI3472YZEC](/sequence-files/IGVFFI3472YZEC/), [IGVFFI0036RVJI](/sequence-files/IGVFFI0036RVJI/) 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/IGVFDS4869FXYY/"
},
{
"category": "missing sequence specification",
"detail": "Measurement set [IGVFDS4869FXYY](/measurement-sets/IGVFDS4869FXYY/) has sequence file(s): [IGVFFI4309IHNT](/sequence-files/IGVFFI4309IHNT/), [IGVFFI2033NCGX](/sequence-files/IGVFFI2033NCGX/), [IGVFFI3960PNJX](/sequence-files/IGVFFI3960PNJX/), [IGVFFI4195XTAZ](/sequence-files/IGVFFI4195XTAZ/), [IGVFFI6572WWXH](/sequence-files/IGVFFI6572WWXH/), [IGVFFI3167OFUE](/sequence-files/IGVFFI3167OFUE/), [IGVFFI3472YZEC](/sequence-files/IGVFFI3472YZEC/), [IGVFFI0036RVJI](/sequence-files/IGVFFI0036RVJI/) 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/IGVFDS4869FXYY/"
}
],
"WARNING": [
{
"category": "missing auxiliary set",
"detail": "Measurement set [IGVFDS4869FXYY](/measurement-sets/IGVFDS4869FXYY/) 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/IGVFDS4869FXYY/"
},
{
"category": "missing targeted genes",
"detail": "Measurement set [IGVFDS4869FXYY](/measurement-sets/IGVFDS4869FXYY/) 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/IGVFDS4869FXYY/"
}
]
},
"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_for": [
{
"@id": "/measurement-sets/IGVFDS2840EKZI/",
"accession": "IGVFDS2840EKZI",
"aliases": [
"jesse-engreitz:230423pPPIFEnformer-Jurkat-Amp_PPIF_promoter-BioRep2-FFrep3-BinC_AmpliconSequencing"
],
"status": "released"
},
{
"@id": "/measurement-sets/IGVFDS4916MNSK/",
"accession": "IGVFDS4916MNSK",
"aliases": [
"jesse-engreitz:230423pPPIFEnformer-Jurkat-Amp_PPIF_promoter-BioRep1-FFrep1-BinB_AmpliconSequencing"
],
"status": "released"
},
{
"@id": "/measurement-sets/IGVFDS5913QKWA/",
"accession": "IGVFDS5913QKWA",
"aliases": [
"jesse-engreitz:230423pPPIFEnformer-Jurkat-Amp_PPIF_promoter-BioRep1-FFrep3-BinA_AmpliconSequencing"
],
"status": "released"
},
{
"@id": "/measurement-sets/IGVFDS0934SYRQ/",
"accession": "IGVFDS0934SYRQ",
"aliases": [
"jesse-engreitz:230423pPPIFEnformer-Jurkat-Amp_PPIF_promoter-BioRep2-FFrep1-BinA_AmpliconSequencing"
],
"status": "released"
},
{
"@id": "/measurement-sets/IGVFDS2609BGAI/",
"accession": "IGVFDS2609BGAI",
"aliases": [
"jesse-engreitz:230423pPPIFEnformer-Jurkat-Amp_PPIF_promoter-BioRep2-FFrep1-BinB_AmpliconSequencing"
],
"status": "released"
},
{
"@id": "/measurement-sets/IGVFDS1199YDYS/",
"accession": "IGVFDS1199YDYS",
"aliases": [
"jesse-engreitz:230423pPPIFEnformer-Jurkat-Amp_PPIF_promoter-BioRep2-FFrep4-FACS_Input_AmpliconSequencing"
],
"status": "released"
},
{
"@id": "/measurement-sets/IGVFDS5504TLBF/",
"accession": "IGVFDS5504TLBF",
"aliases": [
"jesse-engreitz:230423pPPIFEnformer-Jurkat-Amp_PPIF_promoter-BioRep1-FFrep2-FACS_Input_AmpliconSequencing"
],
"status": "released"
},
{
"@id": "/measurement-sets/IGVFDS4623JVYR/",
"accession": "IGVFDS4623JVYR",
"aliases": [
"jesse-engreitz:230423pPPIFEnformer-Jurkat-Amp_PPIF_promoter-BioRep1-FFrep4-FACS_Input_AmpliconSequencing"
],
"status": "released"
},
{
"@id": "/measurement-sets/IGVFDS0022UYQK/",
"accession": "IGVFDS0022UYQK",
"aliases": [
"jesse-engreitz:230423pPPIFEnformer-Jurkat-Amp_PPIF_promoter-BioRep2-FFrep3-BinB_AmpliconSequencing"
],
"status": "released"
},
{
"@id": "/measurement-sets/IGVFDS7163VHFR/",
"accession": "IGVFDS7163VHFR",
"aliases": [
"jesse-engreitz:230423pPPIFEnformer-Jurkat-Amp_PPIF_promoter-BioRep2-FFrep4-BinD_AmpliconSequencing"
],
"status": "released"
},
{
"@id": "/measurement-sets/IGVFDS9080CILW/",
"accession": "IGVFDS9080CILW",
"aliases": [
"jesse-engreitz:230423pPPIFEnformer-Jurkat-Amp_PPIF_promoter-BioRep2-FFrep2-BinD_AmpliconSequencing"
],
"status": "released"
},
{
"@id": "/measurement-sets/IGVFDS0061JZWG/",
"accession": "IGVFDS0061JZWG",
"aliases": [
"jesse-engreitz:230423pPPIFEnformer-Jurkat-Amp_PPIF_promoter-BioRep2-FFrep3-BinD_AmpliconSequencing"
],
"status": "released"
},
{
"@id": "/measurement-sets/IGVFDS5578GVXT/",
"accession": "IGVFDS5578GVXT",
"aliases": [
"jesse-engreitz:230423pPPIFEnformer-Jurkat-Amp_PPIF_promoter-BioRep2-FFrep3-FACS_Input_AmpliconSequencing"
],
"status": "released"
},
{
"@id": "/measurement-sets/IGVFDS8782KHRJ/",
"accession": "IGVFDS8782KHRJ",
"aliases": [
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],
"status": "released"
},
{
"@id": "/measurement-sets/IGVFDS1832KJVS/",
"accession": "IGVFDS1832KJVS",
"aliases": [
"jesse-engreitz:230423pPPIFEnformer-Jurkat-Amp_PPIF_promoter-BioRep2-FFrep1-FACS_Input_AmpliconSequencing"
],
"status": "released"
},
{
"@id": "/measurement-sets/IGVFDS8633UBLT/",
"accession": "IGVFDS8633UBLT",
"aliases": [
"jesse-engreitz:230423pPPIFEnformer-Jurkat-Amp_PPIF_promoter-BioRep2-FFrep3-BinA_AmpliconSequencing"
],
"status": "released"
},
{
"@id": "/measurement-sets/IGVFDS7480YPZN/",
"accession": "IGVFDS7480YPZN",
"aliases": [
"jesse-engreitz:230423pPPIFEnformer-Jurkat-Amp_PPIF_promoter-BioRep1-FFrep1-FACS_Input_AmpliconSequencing"
],
"status": "released"
},
{
"@id": "/measurement-sets/IGVFDS5913KHIA/",
"accession": "IGVFDS5913KHIA",
"aliases": [
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],
"status": "released"
},
{
"@id": "/measurement-sets/IGVFDS1172UDGN/",
"accession": "IGVFDS1172UDGN",
"aliases": [
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],
"status": "released"
},
{
"@id": "/measurement-sets/IGVFDS2157LEAI/",
"accession": "IGVFDS2157LEAI",
"aliases": [
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],
"status": "released"
},
{
"@id": "/measurement-sets/IGVFDS5594RPYL/",
"accession": "IGVFDS5594RPYL",
"aliases": [
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],
"status": "released"
},
{
"@id": "/measurement-sets/IGVFDS4992SJIR/",
"accession": "IGVFDS4992SJIR",
"aliases": [
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],
"status": "released"
},
{
"@id": "/measurement-sets/IGVFDS4758QDZH/",
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],
"status": "released"
},
{
"@id": "/measurement-sets/IGVFDS5704ISFI/",
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],
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},
{
"@id": "/measurement-sets/IGVFDS9602KUWY/",
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"aliases": [
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],
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},
{
"@id": "/measurement-sets/IGVFDS4884AZCV/",
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],
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},
{
"@id": "/measurement-sets/IGVFDS9265YVJX/",
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],
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},
{
"@id": "/measurement-sets/IGVFDS3561FSKT/",
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],
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},
{
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],
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},
{
"@id": "/measurement-sets/IGVFDS4752FLON/",
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],
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},
{
"@id": "/measurement-sets/IGVFDS0595OBOA/",
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],
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},
{
"@id": "/measurement-sets/IGVFDS3485SAPD/",
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},
{
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},
{
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{
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{
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},
{
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},
{
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{
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},
{
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}
],
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"creation_timestamp": "2023-12-13T08:46:37.597561+00:00",
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{
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"aliases": [
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],
"sex": "male",
"status": "released",
"taxa": "Homo sapiens"
}
],
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},
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},
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},
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},
{
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},
{
"@id": "/sequence-files/IGVFFI3167OFUE/",
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"term_name": "Illumina NextSeq 550"
},
"status": "released",
"submitted_file_name": "230423pPPIFEnformerJurkat-Jurkat-PE-NA-Amp-pPPIF-BioRep1-FFRep1_BinNeg-PCRrep2_S402_I2_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI3472YZEC/",
"accession": "IGVFFI3472YZEC",
"aliases": [
"jesse-engreitz:230423pPPIFEnformer-Jurkat-Amp_PPIF_promoter-Jurkat-PE2_Exp2_NegControl-PCRrep2_R1"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2023-12-13T09:29:58.154644+00:00",
"file_format": "fastq",
"file_size": 5990850,
"href": "/sequence-files/IGVFFI3472YZEC/@@download/IGVFFI3472YZEC.fastq.gz",
"s3_uri": "s3://igvf-files/2023/12/13/92d842f7-899a-45ba-8635-a97a31a0798b/IGVFFI3472YZEC.fastq.gz",
"sequencing_platform": {
"@id": "/platform-terms/EFO_0008566/",
"status": "released",
"term_name": "Illumina NextSeq 550"
},
"status": "released",
"submitted_file_name": "230423pPPIFEnformerJurkat-Jurkat-PE-NA-Amp-pPPIF-BioRep1-FFRep1_BinNeg-PCRrep2_S402_R1_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI0036RVJI/",
"accession": "IGVFFI0036RVJI",
"aliases": [
"jesse-engreitz:230423pPPIFEnformer-Jurkat-Amp_PPIF_promoter-Jurkat-PE2_Exp2_NegControl-PCRrep1_R1"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2023-12-13T09:29:00.384211+00:00",
"file_format": "fastq",
"file_size": 5765028,
"href": "/sequence-files/IGVFFI0036RVJI/@@download/IGVFFI0036RVJI.fastq.gz",
"s3_uri": "s3://igvf-files/2023/12/13/2f099ad8-250c-4099-9221-d8fd6c71890a/IGVFFI0036RVJI.fastq.gz",
"sequencing_platform": {
"@id": "/platform-terms/EFO_0008566/",
"status": "released",
"term_name": "Illumina NextSeq 550"
},
"status": "released",
"submitted_file_name": "230423pPPIFEnformerJurkat-Jurkat-PE-NA-Amp-pPPIF-BioRep1-FFRep1_BinNeg-PCRrep1_S401_R1_001.fastq.gz",
"upload_status": "validated"
}
],
"input_for": [
"/analysis-sets/IGVFDS6299IJHG/"
],
"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": "2023-12-20T23:08:10.042104+00:00",
"samples": [
{
"@id": "/in-vitro-systems/IGVFSM3422KXGR/",
"@type": [
"InVitroSystem",
"Biosample",
"Sample",
"Item"
],
"accession": "IGVFSM3422KXGR",
"aliases": [
"jesse-engreitz:230423pPPIFEnformer-Jurkat-Amp_PPIF_promoter-Jurkat-PE2_Exp2_NegControl"
],
"classifications": [
"cell line"
],
"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)",
"taxa": "Homo sapiens"
}
],
"schema_version": "23",
"status": "released",
"submitted_by": {
"@id": "/users/f9e7cd82-a407-4a20-89ee-f4dc668b0cbe/",
"title": "Michael Montgomery"
},
"submitted_files_timestamp": "2023-12-13T09:29:00.384211+00:00",
"summary": "untransfected prime editing Variant-EFFECTS",
"uuid": "c07dac4a-f892-4b8a-bb92-d2d8b7c1b8c2"
}