{
"@context": "/terms/",
"@id": "/measurement-sets/IGVFDS5910HARH/",
"@type": [
"MeasurementSet",
"FileSet",
"Item"
],
"accession": "IGVFDS5910HARH",
"aliases": [
"jesse-engreitz:220228_8merInsertion-THP1-Amp_PPIF_promoter-BioRep1-FFrep1-BinC_AmpliconSequencing"
],
"assay_term": {
"@id": "/assay-terms/OBI_0003661/",
"assay_slims": [
"CRISPR screens"
],
"status": "released",
"term_name": "in vitro CRISPR screen using flow cytometry"
},
"audit": {
"INTERNAL_ACTION": [
{
"category": "mismatched status",
"detail": "Released in vitro system [IGVFSM4143IEHE](/in-vitro-systems/IGVFSM4143IEHE/) 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/IGVFSM4143IEHE/"
},
{
"category": "missing publication",
"detail": "In vitro system [IGVFSM4143IEHE](/in-vitro-systems/IGVFSM4143IEHE/) has no `publications`. Released and archived samples are expected to be associated with a publication.",
"level": 30,
"level_name": "INTERNAL_ACTION",
"name": "audit_sample_missing_publication",
"path": "/in-vitro-systems/IGVFSM4143IEHE/"
},
{
"category": "missing publication",
"detail": "Measurement set [IGVFDS5910HARH](/measurement-sets/IGVFDS5910HARH/) has no `publications`. Released and archived file sets are expected to be associated with a publication.",
"level": 30,
"level_name": "INTERNAL_ACTION",
"name": "audit_file_set_missing_publication",
"path": "/measurement-sets/IGVFDS5910HARH/"
},
{
"category": "missing sequencing kit",
"detail": "Measurement set [IGVFDS5910HARH](/measurement-sets/IGVFDS5910HARH/) has sequence file(s) [IGVFFI7269ZJDT](/sequence-files/IGVFFI7269ZJDT/), [IGVFFI2045QIRT](/sequence-files/IGVFFI2045QIRT/), [IGVFFI6596YCBI](/sequence-files/IGVFFI6596YCBI/), [IGVFFI4034RSJQ](/sequence-files/IGVFFI4034RSJQ/), [IGVFFI4908KRMQ](/sequence-files/IGVFFI4908KRMQ/), [IGVFFI3926YDLF](/sequence-files/IGVFFI3926YDLF/), [IGVFFI1829KCBA](/sequence-files/IGVFFI1829KCBA/), [IGVFFI3890CVPX](/sequence-files/IGVFFI3890CVPX/) which lack specification of a `sequencing_kit`. Sequence files in a file set associated wtih bulk data should specify a sequencing kit.",
"level": 30,
"level_name": "INTERNAL_ACTION",
"name": "audit_inconsistent_sequencing_kit",
"path": "/measurement-sets/IGVFDS5910HARH/"
},
{
"category": "missing sequence specification",
"detail": "Measurement set [IGVFDS5910HARH](/measurement-sets/IGVFDS5910HARH/) has sequence file(s): [IGVFFI7269ZJDT](/sequence-files/IGVFFI7269ZJDT/), [IGVFFI2045QIRT](/sequence-files/IGVFFI2045QIRT/), [IGVFFI6596YCBI](/sequence-files/IGVFFI6596YCBI/), [IGVFFI4034RSJQ](/sequence-files/IGVFFI4034RSJQ/), [IGVFFI4908KRMQ](/sequence-files/IGVFFI4908KRMQ/), [IGVFFI3926YDLF](/sequence-files/IGVFFI3926YDLF/), [IGVFFI1829KCBA](/sequence-files/IGVFFI1829KCBA/), [IGVFFI3890CVPX](/sequence-files/IGVFFI3890CVPX/) which do not have any `seqspecs`. Sequence files in a file set associated with bulk data are expected to link to a sequence specification file.",
"level": 30,
"level_name": "INTERNAL_ACTION",
"name": "audit_missing_seqspec",
"path": "/measurement-sets/IGVFDS5910HARH/"
}
],
"WARNING": [
{
"category": "missing auxiliary set",
"detail": "Measurement set [IGVFDS5910HARH](/measurement-sets/IGVFDS5910HARH/) 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/IGVFDS5910HARH/"
}
]
},
"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"
},
"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"
}
],
"control_file_sets": [
{
"@id": "/measurement-sets/IGVFDS6385JXFZ/",
"accession": "IGVFDS6385JXFZ",
"aliases": [
"jesse-engreitz:220228_8merInsertion-THP1-Amp_PPIF_promoter-THP1-PE2_Exp3_NegControl_AmpliconSequencing"
],
"status": "released"
}
],
"control_for": [],
"creation_timestamp": "2023-12-01T00:01:45.228414+00:00",
"donors": [
{
"@id": "/human-donors/IGVFDO7359LVPI/",
"accession": "IGVFDO7359LVPI",
"aliases": [
"igvf:donor_of_THP1"
],
"sex": "male",
"status": "released",
"taxa": "Homo sapiens"
}
],
"externally_hosted": false,
"file_set_type": "experimental data",
"files": [
{
"@id": "/sequence-files/IGVFFI7269ZJDT/",
"accession": "IGVFFI7269ZJDT",
"aliases": [
"jesse-engreitz:220228_8merInsertion-THP1-Amp_PPIF_promoter-BioRep1-FFrep1-BinC-PCRrep1_I1"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2023-12-05T18:47:44.417705+00:00",
"file_format": "fastq",
"file_size": 15401938,
"href": "/sequence-files/IGVFFI7269ZJDT/@@download/IGVFFI7269ZJDT.fastq.gz",
"s3_uri": "s3://igvf-files/2023/12/05/a238bfde-0b7c-43ff-8fba-0cedbe61f1dd/IGVFFI7269ZJDT.fastq.gz",
"sequencing_platform": {
"@id": "/platform-terms/EFO_0008566/",
"status": "released",
"term_name": "Illumina NextSeq 550"
},
"status": "released",
"submitted_file_name": "220228pPPIF-FFSample-2-D21-pPPIF-Amp-pPPIF-1-1-1-BinC_I1_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI2045QIRT/",
"accession": "IGVFFI2045QIRT",
"aliases": [
"jesse-engreitz:220228_8merInsertion-THP1-Amp_PPIF_promoter-BioRep1-FFrep1-BinC-PCRrep1_R1"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2023-12-05T18:24:17.928959+00:00",
"file_format": "fastq",
"file_size": 42646151,
"href": "/sequence-files/IGVFFI2045QIRT/@@download/IGVFFI2045QIRT.fastq.gz",
"s3_uri": "s3://igvf-files/2023/12/05/910f2092-4df1-4e36-8a91-0d12b3b43964/IGVFFI2045QIRT.fastq.gz",
"sequencing_platform": {
"@id": "/platform-terms/EFO_0008566/",
"status": "released",
"term_name": "Illumina NextSeq 550"
},
"status": "released",
"submitted_file_name": "220228pPPIF-FFSample-2-D21-pPPIF-Amp-pPPIF-1-1-1-BinC_R1_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI6596YCBI/",
"accession": "IGVFFI6596YCBI",
"aliases": [
"jesse-engreitz:220228_8merInsertion-THP1-Amp_PPIF_promoter-BioRep1-FFrep1-BinC-PCRrep1_I2"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2023-12-05T18:58:57.317327+00:00",
"file_format": "fastq",
"file_size": 14380333,
"href": "/sequence-files/IGVFFI6596YCBI/@@download/IGVFFI6596YCBI.fastq.gz",
"s3_uri": "s3://igvf-files/2023/12/05/0c5c4300-7ea8-4df3-9f0c-340c98c0a226/IGVFFI6596YCBI.fastq.gz",
"sequencing_platform": {
"@id": "/platform-terms/EFO_0008566/",
"status": "released",
"term_name": "Illumina NextSeq 550"
},
"status": "released",
"submitted_file_name": "220228pPPIF-FFSample-2-D21-pPPIF-Amp-pPPIF-1-1-1-BinC_I2_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI4034RSJQ/",
"accession": "IGVFFI4034RSJQ",
"aliases": [
"jesse-engreitz:220228_8merInsertion-THP1-Amp_PPIF_promoter-BioRep1-FFrep1-BinC-PCRrep1_R2"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2023-12-05T18:35:42.627034+00:00",
"file_format": "fastq",
"file_size": 76133542,
"href": "/sequence-files/IGVFFI4034RSJQ/@@download/IGVFFI4034RSJQ.fastq.gz",
"s3_uri": "s3://igvf-files/2023/12/05/e0845c26-67e9-43ec-b33d-3a7378d5a621/IGVFFI4034RSJQ.fastq.gz",
"sequencing_platform": {
"@id": "/platform-terms/EFO_0008566/",
"status": "released",
"term_name": "Illumina NextSeq 550"
},
"status": "released",
"submitted_file_name": "220228pPPIF-FFSample-2-D21-pPPIF-Amp-pPPIF-1-1-1-BinC_R2_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI4908KRMQ/",
"accession": "IGVFFI4908KRMQ",
"aliases": [
"jesse-engreitz:220228_8merInsertion-THP1-Amp_PPIF_promoter-BioRep1-FFrep1-BinC-PCRrep2_I1"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2023-12-05T18:53:17.601034+00:00",
"file_format": "fastq",
"file_size": 15372660,
"href": "/sequence-files/IGVFFI4908KRMQ/@@download/IGVFFI4908KRMQ.fastq.gz",
"s3_uri": "s3://igvf-files/2023/12/05/0acb7827-10aa-412c-a6ec-7e8bb8bc8e73/IGVFFI4908KRMQ.fastq.gz",
"sequencing_platform": {
"@id": "/platform-terms/EFO_0008566/",
"status": "released",
"term_name": "Illumina NextSeq 550"
},
"status": "released",
"submitted_file_name": "220228pPPIF-FFSample-2-D21-pPPIF-Amp-pPPIF-1-1-2-BinC_I1_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI3926YDLF/",
"accession": "IGVFFI3926YDLF",
"aliases": [
"jesse-engreitz:220228_8merInsertion-THP1-Amp_PPIF_promoter-BioRep1-FFrep1-BinC-PCRrep2_R2"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2023-12-05T18:41:48.574353+00:00",
"file_format": "fastq",
"file_size": 77294168,
"href": "/sequence-files/IGVFFI3926YDLF/@@download/IGVFFI3926YDLF.fastq.gz",
"s3_uri": "s3://igvf-files/2023/12/05/f0ab64f8-68e1-41bd-8545-bd6f90b7e9a7/IGVFFI3926YDLF.fastq.gz",
"sequencing_platform": {
"@id": "/platform-terms/EFO_0008566/",
"status": "released",
"term_name": "Illumina NextSeq 550"
},
"status": "released",
"submitted_file_name": "220228pPPIF-FFSample-2-D21-pPPIF-Amp-pPPIF-1-1-2-BinC_R2_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI1829KCBA/",
"accession": "IGVFFI1829KCBA",
"aliases": [
"jesse-engreitz:220228_8merInsertion-THP1-Amp_PPIF_promoter-BioRep1-FFrep1-BinC-PCRrep2_R1"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2023-12-05T18:30:02.051609+00:00",
"file_format": "fastq",
"file_size": 42644025,
"href": "/sequence-files/IGVFFI1829KCBA/@@download/IGVFFI1829KCBA.fastq.gz",
"s3_uri": "s3://igvf-files/2023/12/05/23b4ed1c-3cb8-4eda-9176-613d7d2e3802/IGVFFI1829KCBA.fastq.gz",
"sequencing_platform": {
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"status": "released",
"term_name": "Illumina NextSeq 550"
},
"status": "released",
"submitted_file_name": "220228pPPIF-FFSample-2-D21-pPPIF-Amp-pPPIF-1-1-2-BinC_R1_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI3890CVPX/",
"accession": "IGVFFI3890CVPX",
"aliases": [
"jesse-engreitz:220228_8merInsertion-THP1-Amp_PPIF_promoter-BioRep1-FFrep1-BinC-PCRrep2_I2"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2023-12-05T19:04:29.405853+00:00",
"file_format": "fastq",
"file_size": 14601434,
"href": "/sequence-files/IGVFFI3890CVPX/@@download/IGVFFI3890CVPX.fastq.gz",
"s3_uri": "s3://igvf-files/2023/12/05/ca37cc40-aa48-4654-9934-96e43267feb8/IGVFFI3890CVPX.fastq.gz",
"sequencing_platform": {
"@id": "/platform-terms/EFO_0008566/",
"status": "released",
"term_name": "Illumina NextSeq 550"
},
"status": "released",
"submitted_file_name": "220228pPPIF-FFSample-2-D21-pPPIF-Amp-pPPIF-1-1-2-BinC_I2_001.fastq.gz",
"upload_status": "validated"
}
],
"input_for": [
"/analysis-sets/IGVFDS5056OAGR/"
],
"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": "2023-12-20T23:10:24.346934+00:00",
"samples": [
{
"@id": "/in-vitro-systems/IGVFSM4143IEHE/",
"@type": [
"InVitroSystem",
"Biosample",
"Sample",
"Item"
],
"accession": "IGVFSM4143IEHE",
"aliases": [
"jesse-engreitz:220228_8merInsertion-THP1-Amp_PPIF_promoter-BioRep1-FFrep1-BinC"
],
"classifications": [
"cell line"
],
"institutional_certificates": [],
"modifications": [
{
"@id": "/crispr-modifications/fc6bc0b3-a064-47d0-b95d-a9af14bb1624/",
"modality": "prime editing",
"status": "released"
}
],
"sample_terms": [
{
"@id": "/sample-terms/EFO_0001253/",
"@type": [
"SampleTerm",
"OntologyTerm",
"Item"
],
"aliases": [
"igvf:THP-1"
],
"status": "released",
"summary": "THP-1",
"term_name": "THP-1"
}
],
"status": "released",
"summary": "Homo sapiens (male) THP-1 cell line (sorting details: FACS bin for 35-45% expression of PPIF) modified with CRISPR prime editing Sp-nCas9-M-MLV RT (PE2), transduced (lentivirus) with a guide library",
"taxa": "Homo sapiens"
}
],
"schema_version": "26",
"status": "released",
"submitted_by": {
"@id": "/users/f9e7cd82-a407-4a20-89ee-f4dc668b0cbe/",
"title": "Michael Montgomery"
},
"submitted_files_timestamp": "2023-12-05T18:24:17.928959+00:00",
"summary": "CRISPR prime editing Variant-EFFECTS sorted on the expression of PPIF integrating a guide (sgRNA) library targeting sequence variants in a genomic locus",
"targeted_genes": [
{
"@id": "/genes/ENSG00000108179/",
"geneid": "ENSG00000108179",
"name": "peptidylprolyl isomerase F",
"status": "released",
"symbol": "PPIF",
"synonyms": [
"PPIase F",
"peptidylprolyl isomerase F",
"Cyp-D",
"peptidyl-prolyl cis-trans isomerase F, mitochondrial",
"PPIF",
"CyP-M",
"cyclophilin F",
"peptidyl-prolyl cis-trans isomerase, mitochondrial",
"cyclophilin 3",
"cyclophilin D",
"rotamase F",
"mitochondrial cyclophilin",
"CypD",
"CYP3"
]
}
],
"uuid": "360eac0e-c7b3-4b20-bd2b-2e417af84a26"
}