{
"@context": "/terms/",
"@id": "/measurement-sets/IGVFDS1199YDYS/",
"@type": [
"MeasurementSet",
"FileSet",
"Item"
],
"accession": "IGVFDS1199YDYS",
"aliases": [
"jesse-engreitz:230423pPPIFEnformer-Jurkat-Amp_PPIF_promoter-BioRep2-FFrep4-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 [IGVFDS1199YDYS](/measurement-sets/IGVFDS1199YDYS/) has sequence file(s) [IGVFFI6583GVSB](/sequence-files/IGVFFI6583GVSB/), [IGVFFI0510VJAC](/sequence-files/IGVFFI0510VJAC/), [IGVFFI9958ILPL](/sequence-files/IGVFFI9958ILPL/), [IGVFFI7342UGUX](/sequence-files/IGVFFI7342UGUX/), [IGVFFI8964LVQD](/sequence-files/IGVFFI8964LVQD/), [IGVFFI3953TGRE](/sequence-files/IGVFFI3953TGRE/), [IGVFFI1003IQDW](/sequence-files/IGVFFI1003IQDW/), [IGVFFI9524KOKX](/sequence-files/IGVFFI9524KOKX/) 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/IGVFDS1199YDYS/"
},
{
"category": "missing sequence specification",
"detail": "Measurement set [IGVFDS1199YDYS](/measurement-sets/IGVFDS1199YDYS/) has sequence file(s): [IGVFFI6583GVSB](/sequence-files/IGVFFI6583GVSB/), [IGVFFI0510VJAC](/sequence-files/IGVFFI0510VJAC/), [IGVFFI9958ILPL](/sequence-files/IGVFFI9958ILPL/), [IGVFFI7342UGUX](/sequence-files/IGVFFI7342UGUX/), [IGVFFI8964LVQD](/sequence-files/IGVFFI8964LVQD/), [IGVFFI3953TGRE](/sequence-files/IGVFFI3953TGRE/), [IGVFFI1003IQDW](/sequence-files/IGVFFI1003IQDW/), [IGVFFI9524KOKX](/sequence-files/IGVFFI9524KOKX/) 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/IGVFDS1199YDYS/"
},
{
"category": "mismatched status",
"detail": "Released in vitro system [IGVFSM9953KCJZ](/in-vitro-systems/IGVFSM9953KCJZ/) has in progress subobject construct library set [IGVFDS2385DHZO](/construct-library-sets/IGVFDS2385DHZO/).",
"level": 30,
"level_name": "INTERNAL_ACTION",
"name": "audit_item_status",
"path": "/in-vitro-systems/IGVFSM9953KCJZ/"
}
],
"WARNING": [
{
"category": "missing auxiliary set",
"detail": "Measurement set [IGVFDS1199YDYS](/measurement-sets/IGVFDS1199YDYS/) 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/IGVFDS1199YDYS/"
},
{
"category": "missing targeted genes",
"detail": "Measurement set [IGVFDS1199YDYS](/measurement-sets/IGVFDS1199YDYS/) 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/IGVFDS1199YDYS/"
}
]
},
"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/IGVFDS4869FXYY/",
"accession": "IGVFDS4869FXYY",
"aliases": [
"jesse-engreitz:230423pPPIFEnformer-Jurkat-Amp_PPIF_promoter-Jurkat-PE2_Exp2_NegControl_AmpliconSequencing"
],
"status": "released"
}
],
"control_for": [],
"control_type": "unsorted FACS input",
"creation_timestamp": "2023-12-13T08:48:16.102977+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",
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{
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"accession": "IGVFFI6583GVSB",
"aliases": [
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],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2023-12-13T15:58:39.875142+00:00",
"file_format": "fastq",
"file_size": 1756684,
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"s3_uri": "s3://igvf-files/2023/12/13/e5bbbcd6-8833-4dcd-b517-f21ba5376941/IGVFFI6583GVSB.fastq.gz",
"sequencing_platform": {
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"status": "released",
"term_name": "Illumina NextSeq 550"
},
"status": "released",
"submitted_file_name": "230423pPPIFEnformerJurkat-Jurkat-PE-pPPIF_Enformer-Amp-pPPIF-BioRep2-FFRep4_BinAll-PCRrep2_S400_I1_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI0510VJAC/",
"accession": "IGVFFI0510VJAC",
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"jesse-engreitz:230423pPPIFEnformer-Jurkat-Amp_PPIF_promoter-BioRep2-FFrep4-FACS_Input-PCRrep1_I1"
],
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"controlled_access": false,
"creation_timestamp": "2023-12-13T15:57:53.614257+00:00",
"file_format": "fastq",
"file_size": 1753964,
"href": "/sequence-files/IGVFFI0510VJAC/@@download/IGVFFI0510VJAC.fastq.gz",
"s3_uri": "s3://igvf-files/2023/12/13/dd9fb5d5-5802-43ae-b24a-ee1bbaff3059/IGVFFI0510VJAC.fastq.gz",
"sequencing_platform": {
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"status": "released",
"term_name": "Illumina NextSeq 550"
},
"status": "released",
"submitted_file_name": "230423pPPIFEnformerJurkat-Jurkat-PE-pPPIF_Enformer-Amp-pPPIF-BioRep2-FFRep4_BinAll-PCRrep1_S399_I1_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI9958ILPL/",
"accession": "IGVFFI9958ILPL",
"aliases": [
"jesse-engreitz:230423pPPIFEnformer-Jurkat-Amp_PPIF_promoter-BioRep2-FFrep4-FACS_Input-PCRrep2_I2"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2023-12-13T17:01:23.881144+00:00",
"file_format": "fastq",
"file_size": 1736286,
"href": "/sequence-files/IGVFFI9958ILPL/@@download/IGVFFI9958ILPL.fastq.gz",
"s3_uri": "s3://igvf-files/2023/12/13/4de5af97-f3b3-4737-96e7-37550aeef9e3/IGVFFI9958ILPL.fastq.gz",
"sequencing_platform": {
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"status": "released",
"term_name": "Illumina NextSeq 550"
},
"status": "released",
"submitted_file_name": "230423pPPIFEnformerJurkat-Jurkat-PE-pPPIF_Enformer-Amp-pPPIF-BioRep2-FFRep4_BinAll-PCRrep2_S400_I2_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI7342UGUX/",
"accession": "IGVFFI7342UGUX",
"aliases": [
"jesse-engreitz:230423pPPIFEnformer-Jurkat-Amp_PPIF_promoter-BioRep2-FFrep4-FACS_Input-PCRrep1_I2"
],
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"controlled_access": false,
"creation_timestamp": "2023-12-13T17:00:37.393957+00:00",
"file_format": "fastq",
"file_size": 1800776,
"href": "/sequence-files/IGVFFI7342UGUX/@@download/IGVFFI7342UGUX.fastq.gz",
"s3_uri": "s3://igvf-files/2023/12/13/fd43393b-808a-49a8-9cfb-e9820f4feecb/IGVFFI7342UGUX.fastq.gz",
"sequencing_platform": {
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"status": "released",
"term_name": "Illumina NextSeq 550"
},
"status": "released",
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"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI8964LVQD/",
"accession": "IGVFFI8964LVQD",
"aliases": [
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"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2023-12-13T10:25:56.150730+00:00",
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"s3_uri": "s3://igvf-files/2023/12/13/853e579c-88e1-460f-95c0-4a0c00a30612/IGVFFI8964LVQD.fastq.gz",
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"term_name": "Illumina NextSeq 550"
},
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"submitted_file_name": "230423pPPIFEnformerJurkat-Jurkat-PE-pPPIF_Enformer-Amp-pPPIF-BioRep2-FFRep4_BinAll-PCRrep2_S400_R1_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI3953TGRE/",
"accession": "IGVFFI3953TGRE",
"aliases": [
"jesse-engreitz:230423pPPIFEnformer-Jurkat-Amp_PPIF_promoter-BioRep2-FFrep4-FACS_Input-PCRrep1_R2"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2023-12-13T11:30:50.688990+00:00",
"file_format": "fastq",
"file_size": 8852971,
"href": "/sequence-files/IGVFFI3953TGRE/@@download/IGVFFI3953TGRE.fastq.gz",
"s3_uri": "s3://igvf-files/2023/12/13/8a5d2d3b-5610-49a2-8a11-0b870e9dcab1/IGVFFI3953TGRE.fastq.gz",
"sequencing_platform": {
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"status": "released",
"term_name": "Illumina NextSeq 550"
},
"status": "released",
"submitted_file_name": "230423pPPIFEnformerJurkat-Jurkat-PE-pPPIF_Enformer-Amp-pPPIF-BioRep2-FFRep4_BinAll-PCRrep1_S399_R2_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI1003IQDW/",
"accession": "IGVFFI1003IQDW",
"aliases": [
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],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2023-12-13T10:25:08.441288+00:00",
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"status": "released",
"term_name": "Illumina NextSeq 550"
},
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"submitted_file_name": "230423pPPIFEnformerJurkat-Jurkat-PE-pPPIF_Enformer-Amp-pPPIF-BioRep2-FFRep4_BinAll-PCRrep1_S399_R1_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI9524KOKX/",
"accession": "IGVFFI9524KOKX",
"aliases": [
"jesse-engreitz:230423pPPIFEnformer-Jurkat-Amp_PPIF_promoter-BioRep2-FFrep4-FACS_Input-PCRrep2_R2"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2023-12-13T14:55:48.470628+00:00",
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"status": "released",
"term_name": "Illumina NextSeq 550"
},
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"submitted_file_name": "230423pPPIFEnformerJurkat-Jurkat-PE-pPPIF_Enformer-Amp-pPPIF-BioRep2-FFRep4_BinAll-PCRrep2_S400_R2_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": "2023-12-20T23:08:21.738489+00:00",
"samples": [
{
"@id": "/in-vitro-systems/IGVFSM9953KCJZ/",
"@type": [
"InVitroSystem",
"Biosample",
"Sample",
"Item"
],
"accession": "IGVFSM9953KCJZ",
"aliases": [
"jesse-engreitz:230423pPPIFEnformer-Jurkat-Amp_PPIF_promoter-BioRep2-FFrep4-FACS_Input"
],
"classifications": [
"cell line"
],
"construct_library_sets": [
{
"@id": "/construct-library-sets/IGVFDS2385DHZO/",
"accession": "IGVFDS2385DHZO",
"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": "2023-12-13T10:25:08.441288+00:00",
"summary": "unsorted FACS input CRISPR prime editing Variant-EFFECTS integrating a guide (sgRNA) library targeting sequence variants in a genomic locus",
"uuid": "3589df15-63d7-4507-b485-8b2a027bed30"
}