{
"@context": "/terms/",
"@id": "/measurement-sets/IGVFDS7769UXHE/",
"@type": [
"MeasurementSet",
"FileSet",
"Item"
],
"accession": "IGVFDS7769UXHE",
"aliases": [
"jesse-engreitz:220829_8merInsertion-Jurkat_NoStimulation-Amp_PPIF_promoter-BioRep3-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 [IGVFSM8782TWDM](/in-vitro-systems/IGVFSM8782TWDM/) 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/IGVFSM8782TWDM/"
},
{
"category": "missing sequencing kit",
"detail": "Measurement set [IGVFDS7769UXHE](/measurement-sets/IGVFDS7769UXHE/) has sequence file(s) [IGVFFI4401NRHO](/sequence-files/IGVFFI4401NRHO/), [IGVFFI1637UKLW](/sequence-files/IGVFFI1637UKLW/), [IGVFFI6177KAZX](/sequence-files/IGVFFI6177KAZX/), [IGVFFI3971VMYO](/sequence-files/IGVFFI3971VMYO/), [IGVFFI5549VTJR](/sequence-files/IGVFFI5549VTJR/), [IGVFFI0725DJYJ](/sequence-files/IGVFFI0725DJYJ/), [IGVFFI7474YEFV](/sequence-files/IGVFFI7474YEFV/), [IGVFFI2827ASSC](/sequence-files/IGVFFI2827ASSC/) 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/IGVFDS7769UXHE/"
},
{
"category": "missing sequence specification",
"detail": "Measurement set [IGVFDS7769UXHE](/measurement-sets/IGVFDS7769UXHE/) has sequence file(s): [IGVFFI4401NRHO](/sequence-files/IGVFFI4401NRHO/), [IGVFFI1637UKLW](/sequence-files/IGVFFI1637UKLW/), [IGVFFI6177KAZX](/sequence-files/IGVFFI6177KAZX/), [IGVFFI3971VMYO](/sequence-files/IGVFFI3971VMYO/), [IGVFFI5549VTJR](/sequence-files/IGVFFI5549VTJR/), [IGVFFI0725DJYJ](/sequence-files/IGVFFI0725DJYJ/), [IGVFFI7474YEFV](/sequence-files/IGVFFI7474YEFV/), [IGVFFI2827ASSC](/sequence-files/IGVFFI2827ASSC/) 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/IGVFDS7769UXHE/"
}
],
"WARNING": [
{
"category": "missing auxiliary set",
"detail": "Measurement set [IGVFDS7769UXHE](/measurement-sets/IGVFDS7769UXHE/) 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/IGVFDS7769UXHE/"
},
{
"category": "missing targeted genes",
"detail": "Measurement set [IGVFDS7769UXHE](/measurement-sets/IGVFDS7769UXHE/) 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/IGVFDS7769UXHE/"
}
]
},
"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": "2023-11-30T22:47:38.801456+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/IGVFFI4401NRHO/",
"accession": "IGVFFI4401NRHO",
"aliases": [
"jesse-engreitz:220829_8merInsertion-Jurkat_NoStimulation-Amp_PPIF_promoter-BioRep3-FFrep2-FACS_Input-PCRrep2_I2"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2023-12-05T19:30:26.811769+00:00",
"file_format": "fastq",
"file_size": 3326654,
"href": "/sequence-files/IGVFFI4401NRHO/@@download/IGVFFI4401NRHO.fastq.gz",
"s3_uri": "s3://igvf-files/2023/12/05/d9bbda38-9b27-4876-8869-50868d7f9851/IGVFFI4401NRHO.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_S8-BioRep3-FFRep2-BinAll-PCRrep2_S98_I2_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI1637UKLW/",
"accession": "IGVFFI1637UKLW",
"aliases": [
"jesse-engreitz:220829_8merInsertion-Jurkat_NoStimulation-Amp_PPIF_promoter-BioRep3-FFrep2-FACS_Input-PCRrep1_I2"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2023-12-05T19:24:11.822552+00:00",
"file_format": "fastq",
"file_size": 3028576,
"href": "/sequence-files/IGVFFI1637UKLW/@@download/IGVFFI1637UKLW.fastq.gz",
"s3_uri": "s3://igvf-files/2023/12/05/236cbc13-2db9-4130-a9f3-9e72d1aff678/IGVFFI1637UKLW.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_S8-BioRep3-FFRep2-BinAll-PCRrep1_S42_I2_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI6177KAZX/",
"accession": "IGVFFI6177KAZX",
"aliases": [
"jesse-engreitz:220829_8merInsertion-Jurkat_NoStimulation-Amp_PPIF_promoter-BioRep3-FFrep2-FACS_Input-PCRrep1_R1"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2023-12-05T18:45:54.110733+00:00",
"file_format": "fastq",
"file_size": 7370630,
"href": "/sequence-files/IGVFFI6177KAZX/@@download/IGVFFI6177KAZX.fastq.gz",
"s3_uri": "s3://igvf-files/2023/12/05/b7381c7a-9c9e-484f-9d19-b9bbf60b9473/IGVFFI6177KAZX.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_S8-BioRep3-FFRep2-BinAll-PCRrep1_S42_R1_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI3971VMYO/",
"accession": "IGVFFI3971VMYO",
"aliases": [
"jesse-engreitz:220829_8merInsertion-Jurkat_NoStimulation-Amp_PPIF_promoter-BioRep3-FFrep2-FACS_Input-PCRrep2_I1"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2023-12-05T19:17:51.276753+00:00",
"file_format": "fastq",
"file_size": 3333958,
"href": "/sequence-files/IGVFFI3971VMYO/@@download/IGVFFI3971VMYO.fastq.gz",
"s3_uri": "s3://igvf-files/2023/12/05/f14414cd-08c0-48d0-89ad-0402696aedd5/IGVFFI3971VMYO.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_S8-BioRep3-FFRep2-BinAll-PCRrep2_S98_I1_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI5549VTJR/",
"accession": "IGVFFI5549VTJR",
"aliases": [
"jesse-engreitz:220829_8merInsertion-Jurkat_NoStimulation-Amp_PPIF_promoter-BioRep3-FFrep2-FACS_Input-PCRrep2_R2"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2023-12-05T19:05:22.168592+00:00",
"file_format": "fastq",
"file_size": 14885331,
"href": "/sequence-files/IGVFFI5549VTJR/@@download/IGVFFI5549VTJR.fastq.gz",
"s3_uri": "s3://igvf-files/2023/12/05/0c8576b6-72ef-417b-9ab3-695d584abb6c/IGVFFI5549VTJR.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_S8-BioRep3-FFRep2-BinAll-PCRrep2_S98_R2_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI0725DJYJ/",
"accession": "IGVFFI0725DJYJ",
"aliases": [
"jesse-engreitz:220829_8merInsertion-Jurkat_NoStimulation-Amp_PPIF_promoter-BioRep3-FFrep2-FACS_Input-PCRrep1_R2"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2023-12-05T18:58:44.855012+00:00",
"file_format": "fastq",
"file_size": 13717774,
"href": "/sequence-files/IGVFFI0725DJYJ/@@download/IGVFFI0725DJYJ.fastq.gz",
"s3_uri": "s3://igvf-files/2023/12/05/74395386-fe7c-42e4-a231-17f7953770b1/IGVFFI0725DJYJ.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_S8-BioRep3-FFRep2-BinAll-PCRrep1_S42_R2_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI7474YEFV/",
"accession": "IGVFFI7474YEFV",
"aliases": [
"jesse-engreitz:220829_8merInsertion-Jurkat_NoStimulation-Amp_PPIF_promoter-BioRep3-FFrep2-FACS_Input-PCRrep2_R1"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2023-12-05T18:52:12.072600+00:00",
"file_format": "fastq",
"file_size": 7985167,
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"s3_uri": "s3://igvf-files/2023/12/05/d5cdada3-26f8-4d7c-a41e-6c694f1d28be/IGVFFI7474YEFV.fastq.gz",
"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_S8-BioRep3-FFRep2-BinAll-PCRrep2_S98_R1_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI2827ASSC/",
"accession": "IGVFFI2827ASSC",
"aliases": [
"jesse-engreitz:220829_8merInsertion-Jurkat_NoStimulation-Amp_PPIF_promoter-BioRep3-FFrep2-FACS_Input-PCRrep1_I1"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2023-12-05T19:11:35.970902+00:00",
"file_format": "fastq",
"file_size": 3069669,
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"s3_uri": "s3://igvf-files/2023/12/05/b54ff226-9aad-4eaf-91fa-edc84b28e43f/IGVFFI2827ASSC.fastq.gz",
"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_S8-BioRep3-FFRep2-BinAll-PCRrep1_S42_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": "2023-12-20T23:04:14.668840+00:00",
"samples": [
{
"@id": "/in-vitro-systems/IGVFSM8782TWDM/",
"@type": [
"InVitroSystem",
"Biosample",
"Sample",
"Item"
],
"accession": "IGVFSM8782TWDM",
"aliases": [
"jesse-engreitz:220829_8merInsertion-Jurkat_NoStimulation-Amp_PPIF_promoter-BioRep3-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": "2023-12-05T18:45:54.110733+00:00",
"summary": "unsorted FACS input CRISPR prime editing Variant-EFFECTS integrating a guide (sgRNA) library targeting sequence variants in a genomic locus",
"uuid": "054f381a-a751-43d8-8d38-39c8059cb775"
}