{
"@context": "/terms/",
"@id": "/measurement-sets/IGVFDS2324AQUM/",
"@type": [
"MeasurementSet",
"FileSet",
"Item"
],
"accession": "IGVFDS2324AQUM",
"aliases": [
"jesse-engreitz:220829_8merInsertion-Jurkat_NoStimulation-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 [IGVFSM2273ETFB](/in-vitro-systems/IGVFSM2273ETFB/) 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/IGVFSM2273ETFB/"
},
{
"category": "missing sequencing kit",
"detail": "Measurement set [IGVFDS2324AQUM](/measurement-sets/IGVFDS2324AQUM/) has sequence file(s) [IGVFFI5062LEQX](/sequence-files/IGVFFI5062LEQX/), [IGVFFI4834LGBB](/sequence-files/IGVFFI4834LGBB/), [IGVFFI1869FICF](/sequence-files/IGVFFI1869FICF/), [IGVFFI0375HIBX](/sequence-files/IGVFFI0375HIBX/), [IGVFFI5377HZWM](/sequence-files/IGVFFI5377HZWM/), [IGVFFI2300DRKP](/sequence-files/IGVFFI2300DRKP/), [IGVFFI6787WNJO](/sequence-files/IGVFFI6787WNJO/), [IGVFFI1622FWWP](/sequence-files/IGVFFI1622FWWP/) 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/IGVFDS2324AQUM/"
},
{
"category": "missing sequence specification",
"detail": "Measurement set [IGVFDS2324AQUM](/measurement-sets/IGVFDS2324AQUM/) has sequence file(s): [IGVFFI5062LEQX](/sequence-files/IGVFFI5062LEQX/), [IGVFFI4834LGBB](/sequence-files/IGVFFI4834LGBB/), [IGVFFI1869FICF](/sequence-files/IGVFFI1869FICF/), [IGVFFI0375HIBX](/sequence-files/IGVFFI0375HIBX/), [IGVFFI5377HZWM](/sequence-files/IGVFFI5377HZWM/), [IGVFFI2300DRKP](/sequence-files/IGVFFI2300DRKP/), [IGVFFI6787WNJO](/sequence-files/IGVFFI6787WNJO/), [IGVFFI1622FWWP](/sequence-files/IGVFFI1622FWWP/) 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/IGVFDS2324AQUM/"
}
],
"WARNING": [
{
"category": "missing auxiliary set",
"detail": "Measurement set [IGVFDS2324AQUM](/measurement-sets/IGVFDS2324AQUM/) 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/IGVFDS2324AQUM/"
},
{
"category": "missing targeted genes",
"detail": "Measurement set [IGVFDS2324AQUM](/measurement-sets/IGVFDS2324AQUM/) 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/IGVFDS2324AQUM/"
}
]
},
"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": "2023-11-30T22:47:15.815394+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/IGVFFI5062LEQX/",
"accession": "IGVFFI5062LEQX",
"aliases": [
"jesse-engreitz:220829_8merInsertion-Jurkat_NoStimulation-Amp_PPIF_promoter-BioRep2-FFrep1-FACS_Input-PCRrep1_I1"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2023-12-05T19:08:32.636866+00:00",
"file_format": "fastq",
"file_size": 3131993,
"href": "/sequence-files/IGVFFI5062LEQX/@@download/IGVFFI5062LEQX.fastq.gz",
"s3_uri": "s3://igvf-files/2023/12/05/4896e34a-70c0-46fa-9671-b33a37d83367/IGVFFI5062LEQX.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_S5-BioRep2-FFRep1-BinAll-PCRrep1_S21_I1_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI4834LGBB/",
"accession": "IGVFFI4834LGBB",
"aliases": [
"jesse-engreitz:220829_8merInsertion-Jurkat_NoStimulation-Amp_PPIF_promoter-BioRep2-FFrep1-FACS_Input-PCRrep1_R2"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2023-12-05T18:55:32.424897+00:00",
"file_format": "fastq",
"file_size": 13534333,
"href": "/sequence-files/IGVFFI4834LGBB/@@download/IGVFFI4834LGBB.fastq.gz",
"s3_uri": "s3://igvf-files/2023/12/05/c5064f56-35b0-4f50-9dc0-5af318ec9a8f/IGVFFI4834LGBB.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_S5-BioRep2-FFRep1-BinAll-PCRrep1_S21_R2_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI1869FICF/",
"accession": "IGVFFI1869FICF",
"aliases": [
"jesse-engreitz:220829_8merInsertion-Jurkat_NoStimulation-Amp_PPIF_promoter-BioRep2-FFrep1-FACS_Input-PCRrep1_I2"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2023-12-05T19:21:04.714034+00:00",
"file_format": "fastq",
"file_size": 3021903,
"href": "/sequence-files/IGVFFI1869FICF/@@download/IGVFFI1869FICF.fastq.gz",
"s3_uri": "s3://igvf-files/2023/12/05/5f0edf4b-3f9c-4920-b1cc-afd8ef3af519/IGVFFI1869FICF.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_S5-BioRep2-FFRep1-BinAll-PCRrep1_S21_I2_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI0375HIBX/",
"accession": "IGVFFI0375HIBX",
"aliases": [
"jesse-engreitz:220829_8merInsertion-Jurkat_NoStimulation-Amp_PPIF_promoter-BioRep2-FFrep1-FACS_Input-PCRrep2_R2"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2023-12-05T19:02:10.267390+00:00",
"file_format": "fastq",
"file_size": 12235415,
"href": "/sequence-files/IGVFFI0375HIBX/@@download/IGVFFI0375HIBX.fastq.gz",
"s3_uri": "s3://igvf-files/2023/12/05/575a1e95-5071-4b67-a6cc-30ca09217ab1/IGVFFI0375HIBX.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_S5-BioRep2-FFRep1-BinAll-PCRrep2_S77_R2_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI5377HZWM/",
"accession": "IGVFFI5377HZWM",
"aliases": [
"jesse-engreitz:220829_8merInsertion-Jurkat_NoStimulation-Amp_PPIF_promoter-BioRep2-FFrep1-FACS_Input-PCRrep2_R1"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2023-12-05T18:49:07.830047+00:00",
"file_format": "fastq",
"file_size": 6696036,
"href": "/sequence-files/IGVFFI5377HZWM/@@download/IGVFFI5377HZWM.fastq.gz",
"s3_uri": "s3://igvf-files/2023/12/05/723f3049-72cd-42ea-b6a3-511f78bb0c13/IGVFFI5377HZWM.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_S5-BioRep2-FFRep1-BinAll-PCRrep2_S77_R1_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI2300DRKP/",
"accession": "IGVFFI2300DRKP",
"aliases": [
"jesse-engreitz:220829_8merInsertion-Jurkat_NoStimulation-Amp_PPIF_promoter-BioRep2-FFrep1-FACS_Input-PCRrep2_I1"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2023-12-05T19:14:48.178956+00:00",
"file_format": "fastq",
"file_size": 2796380,
"href": "/sequence-files/IGVFFI2300DRKP/@@download/IGVFFI2300DRKP.fastq.gz",
"s3_uri": "s3://igvf-files/2023/12/05/89515619-49e2-49cc-a96b-cf915529b422/IGVFFI2300DRKP.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_S5-BioRep2-FFRep1-BinAll-PCRrep2_S77_I1_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI6787WNJO/",
"accession": "IGVFFI6787WNJO",
"aliases": [
"jesse-engreitz:220829_8merInsertion-Jurkat_NoStimulation-Amp_PPIF_promoter-BioRep2-FFrep1-FACS_Input-PCRrep1_R1"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2023-12-05T18:42:49.113900+00:00",
"file_format": "fastq",
"file_size": 7378054,
"href": "/sequence-files/IGVFFI6787WNJO/@@download/IGVFFI6787WNJO.fastq.gz",
"s3_uri": "s3://igvf-files/2023/12/05/1421fdfb-7ed7-43ba-b730-82cc06a8bbec/IGVFFI6787WNJO.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_S5-BioRep2-FFRep1-BinAll-PCRrep1_S21_R1_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI1622FWWP/",
"accession": "IGVFFI1622FWWP",
"aliases": [
"jesse-engreitz:220829_8merInsertion-Jurkat_NoStimulation-Amp_PPIF_promoter-BioRep2-FFrep1-FACS_Input-PCRrep2_I2"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2023-12-05T19:27:23.398316+00:00",
"file_format": "fastq",
"file_size": 2748408,
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"s3_uri": "s3://igvf-files/2023/12/05/4e7d9976-1714-4f62-9504-db5854447a0e/IGVFFI1622FWWP.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_S5-BioRep2-FFRep1-BinAll-PCRrep2_S77_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": "2023-12-20T23:05:00.045517+00:00",
"samples": [
{
"@id": "/in-vitro-systems/IGVFSM2273ETFB/",
"@type": [
"InVitroSystem",
"Biosample",
"Sample",
"Item"
],
"accession": "IGVFSM2273ETFB",
"aliases": [
"jesse-engreitz:220829_8merInsertion-Jurkat_NoStimulation-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 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": "2023-12-05T18:42:49.113900+00:00",
"summary": "unsorted FACS input CRISPR prime editing Variant-EFFECTS integrating a guide (sgRNA) library targeting sequence variants in a genomic locus",
"uuid": "5f846c06-fe83-40ed-8505-c5ac9e184584"
}