{
"@context": "/terms/",
"@id": "/measurement-sets/IGVFDS9567MJGD/",
"@type": [
"MeasurementSet",
"FileSet",
"Item"
],
"accession": "IGVFDS9567MJGD",
"aliases": [
"jesse-engreitz:220829_8merInsertion-Jurkat_NoStimulation-Amp_PPIF_promoter-BioRep2-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": "missing sequencing kit",
"detail": "Measurement set [IGVFDS9567MJGD](/measurement-sets/IGVFDS9567MJGD/) has sequence file(s) [IGVFFI8093MRHK](/sequence-files/IGVFFI8093MRHK/), [IGVFFI7571SVTN](/sequence-files/IGVFFI7571SVTN/), [IGVFFI2192FIJO](/sequence-files/IGVFFI2192FIJO/), [IGVFFI7782NPYX](/sequence-files/IGVFFI7782NPYX/), [IGVFFI1669IEVQ](/sequence-files/IGVFFI1669IEVQ/), [IGVFFI8115IIVR](/sequence-files/IGVFFI8115IIVR/), [IGVFFI3885HURV](/sequence-files/IGVFFI3885HURV/), [IGVFFI0993MBCL](/sequence-files/IGVFFI0993MBCL/) 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/IGVFDS9567MJGD/"
},
{
"category": "missing sequence specification",
"detail": "Measurement set [IGVFDS9567MJGD](/measurement-sets/IGVFDS9567MJGD/) has sequence file(s): [IGVFFI8093MRHK](/sequence-files/IGVFFI8093MRHK/), [IGVFFI7571SVTN](/sequence-files/IGVFFI7571SVTN/), [IGVFFI2192FIJO](/sequence-files/IGVFFI2192FIJO/), [IGVFFI7782NPYX](/sequence-files/IGVFFI7782NPYX/), [IGVFFI1669IEVQ](/sequence-files/IGVFFI1669IEVQ/), [IGVFFI8115IIVR](/sequence-files/IGVFFI8115IIVR/), [IGVFFI3885HURV](/sequence-files/IGVFFI3885HURV/), [IGVFFI0993MBCL](/sequence-files/IGVFFI0993MBCL/) 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/IGVFDS9567MJGD/"
},
{
"category": "mismatched status",
"detail": "Released in vitro system [IGVFSM9237MPMD](/in-vitro-systems/IGVFSM9237MPMD/) 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/IGVFSM9237MPMD/"
}
],
"WARNING": [
{
"category": "missing auxiliary set",
"detail": "Measurement set [IGVFDS9567MJGD](/measurement-sets/IGVFDS9567MJGD/) 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/IGVFDS9567MJGD/"
},
{
"category": "missing targeted genes",
"detail": "Measurement set [IGVFDS9567MJGD](/measurement-sets/IGVFDS9567MJGD/) 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/IGVFDS9567MJGD/"
}
]
},
"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": "2023-11-30T22:47:23.325849+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/IGVFFI8093MRHK/",
"accession": "IGVFFI8093MRHK",
"aliases": [
"jesse-engreitz:220829_8merInsertion-Jurkat_NoStimulation-Amp_PPIF_promoter-BioRep2-FFrep2-FACS_Input-PCRrep2_R2"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2023-12-05T19:03:13.893373+00:00",
"file_format": "fastq",
"file_size": 15320748,
"href": "/sequence-files/IGVFFI8093MRHK/@@download/IGVFFI8093MRHK.fastq.gz",
"s3_uri": "s3://igvf-files/2023/12/05/b0aeda64-7c45-43e9-a311-5ab149094360/IGVFFI8093MRHK.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_S6-BioRep2-FFRep2-BinAll-PCRrep2_S84_R2_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI7571SVTN/",
"accession": "IGVFFI7571SVTN",
"aliases": [
"jesse-engreitz:220829_8merInsertion-Jurkat_NoStimulation-Amp_PPIF_promoter-BioRep2-FFrep2-FACS_Input-PCRrep2_I1"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2023-12-05T19:15:49.399260+00:00",
"file_format": "fastq",
"file_size": 3656318,
"href": "/sequence-files/IGVFFI7571SVTN/@@download/IGVFFI7571SVTN.fastq.gz",
"s3_uri": "s3://igvf-files/2023/12/05/e56faeb6-44aa-42df-bc0a-2dfa287ea9d8/IGVFFI7571SVTN.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_S6-BioRep2-FFRep2-BinAll-PCRrep2_S84_I1_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI2192FIJO/",
"accession": "IGVFFI2192FIJO",
"aliases": [
"jesse-engreitz:220829_8merInsertion-Jurkat_NoStimulation-Amp_PPIF_promoter-BioRep2-FFrep2-FACS_Input-PCRrep1_R1"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2023-12-05T18:43:50.379127+00:00",
"file_format": "fastq",
"file_size": 7816306,
"href": "/sequence-files/IGVFFI2192FIJO/@@download/IGVFFI2192FIJO.fastq.gz",
"s3_uri": "s3://igvf-files/2023/12/05/66fa4730-49bb-44e9-9751-fc252beb58db/IGVFFI2192FIJO.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_S6-BioRep2-FFRep2-BinAll-PCRrep1_S28_R1_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI7782NPYX/",
"accession": "IGVFFI7782NPYX",
"aliases": [
"jesse-engreitz:220829_8merInsertion-Jurkat_NoStimulation-Amp_PPIF_promoter-BioRep2-FFrep2-FACS_Input-PCRrep2_R1"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2023-12-05T18:50:09.351302+00:00",
"file_format": "fastq",
"file_size": 8351976,
"href": "/sequence-files/IGVFFI7782NPYX/@@download/IGVFFI7782NPYX.fastq.gz",
"s3_uri": "s3://igvf-files/2023/12/05/d4d2f221-b151-479d-814e-9c13f9ec320e/IGVFFI7782NPYX.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_S6-BioRep2-FFRep2-BinAll-PCRrep2_S84_R1_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI1669IEVQ/",
"accession": "IGVFFI1669IEVQ",
"aliases": [
"jesse-engreitz:220829_8merInsertion-Jurkat_NoStimulation-Amp_PPIF_promoter-BioRep2-FFrep2-FACS_Input-PCRrep1_I2"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2023-12-05T19:22:05.964289+00:00",
"file_format": "fastq",
"file_size": 3185181,
"href": "/sequence-files/IGVFFI1669IEVQ/@@download/IGVFFI1669IEVQ.fastq.gz",
"s3_uri": "s3://igvf-files/2023/12/05/2b43a7c2-d905-4ed8-aa3e-fdf9f4d40e9c/IGVFFI1669IEVQ.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_S6-BioRep2-FFRep2-BinAll-PCRrep1_S28_I2_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI8115IIVR/",
"accession": "IGVFFI8115IIVR",
"aliases": [
"jesse-engreitz:220829_8merInsertion-Jurkat_NoStimulation-Amp_PPIF_promoter-BioRep2-FFrep2-FACS_Input-PCRrep1_I1"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2023-12-05T19:09:33.779113+00:00",
"file_format": "fastq",
"file_size": 3304790,
"href": "/sequence-files/IGVFFI8115IIVR/@@download/IGVFFI8115IIVR.fastq.gz",
"s3_uri": "s3://igvf-files/2023/12/05/676fc7b0-037f-4e56-82eb-13fc7877f009/IGVFFI8115IIVR.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_S6-BioRep2-FFRep2-BinAll-PCRrep1_S28_I1_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI3885HURV/",
"accession": "IGVFFI3885HURV",
"aliases": [
"jesse-engreitz:220829_8merInsertion-Jurkat_NoStimulation-Amp_PPIF_promoter-BioRep2-FFrep2-FACS_Input-PCRrep2_I2"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2023-12-05T19:28:24.923452+00:00",
"file_format": "fastq",
"file_size": 3409204,
"href": "/sequence-files/IGVFFI3885HURV/@@download/IGVFFI3885HURV.fastq.gz",
"s3_uri": "s3://igvf-files/2023/12/05/54cf9040-9525-4d03-8910-13bd4bd872da/IGVFFI3885HURV.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_S6-BioRep2-FFRep2-BinAll-PCRrep2_S84_I2_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI0993MBCL/",
"accession": "IGVFFI0993MBCL",
"aliases": [
"jesse-engreitz:220829_8merInsertion-Jurkat_NoStimulation-Amp_PPIF_promoter-BioRep2-FFrep2-FACS_Input-PCRrep1_R2"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2023-12-05T18:56:36.690027+00:00",
"file_format": "fastq",
"file_size": 14303642,
"href": "/sequence-files/IGVFFI0993MBCL/@@download/IGVFFI0993MBCL.fastq.gz",
"s3_uri": "s3://igvf-files/2023/12/05/17d97045-bac4-4d1b-b1d2-129436d8c203/IGVFFI0993MBCL.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_S6-BioRep2-FFRep2-BinAll-PCRrep1_S28_R2_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": "2023-12-20T23:04:10.855140+00:00",
"samples": [
{
"@id": "/in-vitro-systems/IGVFSM9237MPMD/",
"@type": [
"InVitroSystem",
"Biosample",
"Sample",
"Item"
],
"accession": "IGVFSM9237MPMD",
"aliases": [
"jesse-engreitz:220829_8merInsertion-Jurkat_NoStimulation-Amp_PPIF_promoter-BioRep2-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": "2023-12-05T18:43:50.379127+00:00",
"summary": "unsorted FACS input CRISPR prime editing Variant-EFFECTS integrating a guide (sgRNA) library targeting sequence variants in a genomic locus",
"uuid": "3ff6cad1-b699-44d8-9086-2f100fbeaf89"
}