{
"@context": "/terms/",
"@id": "/measurement-sets/IGVFDS0735XAQF/",
"@type": [
"MeasurementSet",
"FileSet",
"Item"
],
"accession": "IGVFDS0735XAQF",
"aliases": [
"jesse-engreitz:220228_8merInsertion-THP1-Amp_PPIF_promoter-BioRep1-FFrep3-BinE_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": "missing publication",
"detail": "Measurement set [IGVFDS0735XAQF](/measurement-sets/IGVFDS0735XAQF/) 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/IGVFDS0735XAQF/"
},
{
"category": "missing sequencing kit",
"detail": "Measurement set [IGVFDS0735XAQF](/measurement-sets/IGVFDS0735XAQF/) has sequence file(s) [IGVFFI2236GWTP](/sequence-files/IGVFFI2236GWTP/), [IGVFFI7658TSHW](/sequence-files/IGVFFI7658TSHW/), [IGVFFI5522GEKI](/sequence-files/IGVFFI5522GEKI/), [IGVFFI9987YUSC](/sequence-files/IGVFFI9987YUSC/), [IGVFFI8448GTWB](/sequence-files/IGVFFI8448GTWB/), [IGVFFI8069SXTM](/sequence-files/IGVFFI8069SXTM/), [IGVFFI8368INFN](/sequence-files/IGVFFI8368INFN/), [IGVFFI9936XGST](/sequence-files/IGVFFI9936XGST/) 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/IGVFDS0735XAQF/"
},
{
"category": "missing sequence specification",
"detail": "Measurement set [IGVFDS0735XAQF](/measurement-sets/IGVFDS0735XAQF/) has sequence file(s): [IGVFFI2236GWTP](/sequence-files/IGVFFI2236GWTP/), [IGVFFI7658TSHW](/sequence-files/IGVFFI7658TSHW/), [IGVFFI5522GEKI](/sequence-files/IGVFFI5522GEKI/), [IGVFFI9987YUSC](/sequence-files/IGVFFI9987YUSC/), [IGVFFI8448GTWB](/sequence-files/IGVFFI8448GTWB/), [IGVFFI8069SXTM](/sequence-files/IGVFFI8069SXTM/), [IGVFFI8368INFN](/sequence-files/IGVFFI8368INFN/), [IGVFFI9936XGST](/sequence-files/IGVFFI9936XGST/) 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/IGVFDS0735XAQF/"
},
{
"category": "mismatched status",
"detail": "Released in vitro system [IGVFSM1989ECAN](/in-vitro-systems/IGVFSM1989ECAN/) 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/IGVFSM1989ECAN/"
},
{
"category": "missing publication",
"detail": "In vitro system [IGVFSM1989ECAN](/in-vitro-systems/IGVFSM1989ECAN/) 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/IGVFSM1989ECAN/"
}
],
"WARNING": [
{
"category": "missing auxiliary set",
"detail": "Measurement set [IGVFDS0735XAQF](/measurement-sets/IGVFDS0735XAQF/) 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/IGVFDS0735XAQF/"
}
]
},
"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": "2023-11-30T22:46:06.363229+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/IGVFFI2236GWTP/",
"accession": "IGVFFI2236GWTP",
"aliases": [
"jesse-engreitz:220228_8merInsertion-THP1-Amp_PPIF_promoter-BioRep1-FFrep3-BinE-PCRrep2_I1"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2023-12-05T18:55:44.098012+00:00",
"file_format": "fastq",
"file_size": 14374753,
"href": "/sequence-files/IGVFFI2236GWTP/@@download/IGVFFI2236GWTP.fastq.gz",
"s3_uri": "s3://igvf-files/2023/12/05/6c8bba44-5aff-4b7d-b0fd-6ffcdcc23f96/IGVFFI2236GWTP.fastq.gz",
"sequencing_platform": {
"@id": "/platform-terms/EFO_0008566/",
"status": "released",
"term_name": "Illumina NextSeq 550"
},
"status": "released",
"submitted_file_name": "220228pPPIF-FFSample-4-D21-pPPIF-Amp-pPPIF-1-3-2-BinE_I1_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI7658TSHW/",
"accession": "IGVFFI7658TSHW",
"aliases": [
"jesse-engreitz:220228_8merInsertion-THP1-Amp_PPIF_promoter-BioRep1-FFrep3-BinE-PCRrep1_R1"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2023-12-05T18:26:47.833520+00:00",
"file_format": "fastq",
"file_size": 40193381,
"href": "/sequence-files/IGVFFI7658TSHW/@@download/IGVFFI7658TSHW.fastq.gz",
"s3_uri": "s3://igvf-files/2023/12/05/64db6d05-951d-4aec-a3ef-87fa847c177e/IGVFFI7658TSHW.fastq.gz",
"sequencing_platform": {
"@id": "/platform-terms/EFO_0008566/",
"status": "released",
"term_name": "Illumina NextSeq 550"
},
"status": "released",
"submitted_file_name": "220228pPPIF-FFSample-4-D21-pPPIF-Amp-pPPIF-1-3-1-BinE_R1_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI5522GEKI/",
"accession": "IGVFFI5522GEKI",
"aliases": [
"jesse-engreitz:220228_8merInsertion-THP1-Amp_PPIF_promoter-BioRep1-FFrep3-BinE-PCRrep2_R2"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2023-12-05T18:44:29.606388+00:00",
"file_format": "fastq",
"file_size": 70159029,
"href": "/sequence-files/IGVFFI5522GEKI/@@download/IGVFFI5522GEKI.fastq.gz",
"s3_uri": "s3://igvf-files/2023/12/05/66bede63-3ad3-4e19-b17b-a26863cdcb74/IGVFFI5522GEKI.fastq.gz",
"sequencing_platform": {
"@id": "/platform-terms/EFO_0008566/",
"status": "released",
"term_name": "Illumina NextSeq 550"
},
"status": "released",
"submitted_file_name": "220228pPPIF-FFSample-4-D21-pPPIF-Amp-pPPIF-1-3-2-BinE_R2_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI9987YUSC/",
"accession": "IGVFFI9987YUSC",
"aliases": [
"jesse-engreitz:220228_8merInsertion-THP1-Amp_PPIF_promoter-BioRep1-FFrep3-BinE-PCRrep2_R1"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2023-12-05T18:32:32.137198+00:00",
"file_format": "fastq",
"file_size": 38735257,
"href": "/sequence-files/IGVFFI9987YUSC/@@download/IGVFFI9987YUSC.fastq.gz",
"s3_uri": "s3://igvf-files/2023/12/05/1aeb37fe-4bf9-481d-b12c-ae3c5d316ecf/IGVFFI9987YUSC.fastq.gz",
"sequencing_platform": {
"@id": "/platform-terms/EFO_0008566/",
"status": "released",
"term_name": "Illumina NextSeq 550"
},
"status": "released",
"submitted_file_name": "220228pPPIF-FFSample-4-D21-pPPIF-Amp-pPPIF-1-3-2-BinE_R1_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI8448GTWB/",
"accession": "IGVFFI8448GTWB",
"aliases": [
"jesse-engreitz:220228_8merInsertion-THP1-Amp_PPIF_promoter-BioRep1-FFrep3-BinE-PCRrep1_I2"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2023-12-05T19:01:25.316098+00:00",
"file_format": "fastq",
"file_size": 13645986,
"href": "/sequence-files/IGVFFI8448GTWB/@@download/IGVFFI8448GTWB.fastq.gz",
"s3_uri": "s3://igvf-files/2023/12/05/c54ea2ea-af00-4c80-bfa6-ad67069e0c2a/IGVFFI8448GTWB.fastq.gz",
"sequencing_platform": {
"@id": "/platform-terms/EFO_0008566/",
"status": "released",
"term_name": "Illumina NextSeq 550"
},
"status": "released",
"submitted_file_name": "220228pPPIF-FFSample-4-D21-pPPIF-Amp-pPPIF-1-3-1-BinE_I2_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI8069SXTM/",
"accession": "IGVFFI8069SXTM",
"aliases": [
"jesse-engreitz:220228_8merInsertion-THP1-Amp_PPIF_promoter-BioRep1-FFrep3-BinE-PCRrep1_R2"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2023-12-05T18:38:29.859201+00:00",
"file_format": "fastq",
"file_size": 72049358,
"href": "/sequence-files/IGVFFI8069SXTM/@@download/IGVFFI8069SXTM.fastq.gz",
"s3_uri": "s3://igvf-files/2023/12/05/f19e0d8a-cc6b-401d-9fbe-f604e79d8601/IGVFFI8069SXTM.fastq.gz",
"sequencing_platform": {
"@id": "/platform-terms/EFO_0008566/",
"status": "released",
"term_name": "Illumina NextSeq 550"
},
"status": "released",
"submitted_file_name": "220228pPPIF-FFSample-4-D21-pPPIF-Amp-pPPIF-1-3-1-BinE_R2_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI8368INFN/",
"accession": "IGVFFI8368INFN",
"aliases": [
"jesse-engreitz:220228_8merInsertion-THP1-Amp_PPIF_promoter-BioRep1-FFrep3-BinE-PCRrep2_I2"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2023-12-05T19:06:59.827695+00:00",
"file_format": "fastq",
"file_size": 13348897,
"href": "/sequence-files/IGVFFI8368INFN/@@download/IGVFFI8368INFN.fastq.gz",
"s3_uri": "s3://igvf-files/2023/12/05/564cfca7-f33a-4ce0-bb58-43932d214a4b/IGVFFI8368INFN.fastq.gz",
"sequencing_platform": {
"@id": "/platform-terms/EFO_0008566/",
"status": "released",
"term_name": "Illumina NextSeq 550"
},
"status": "released",
"submitted_file_name": "220228pPPIF-FFSample-4-D21-pPPIF-Amp-pPPIF-1-3-2-BinE_I2_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI9936XGST/",
"accession": "IGVFFI9936XGST",
"aliases": [
"jesse-engreitz:220228_8merInsertion-THP1-Amp_PPIF_promoter-BioRep1-FFrep3-BinE-PCRrep1_I1"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2023-12-05T18:50:11.098945+00:00",
"file_format": "fastq",
"file_size": 14582893,
"href": "/sequence-files/IGVFFI9936XGST/@@download/IGVFFI9936XGST.fastq.gz",
"s3_uri": "s3://igvf-files/2023/12/05/ef26219d-7a2b-4c68-8d7b-f1beed949245/IGVFFI9936XGST.fastq.gz",
"sequencing_platform": {
"@id": "/platform-terms/EFO_0008566/",
"status": "released",
"term_name": "Illumina NextSeq 550"
},
"status": "released",
"submitted_file_name": "220228pPPIF-FFSample-4-D21-pPPIF-Amp-pPPIF-1-3-1-BinE_I1_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": "2023-12-20T23:10:28.041416+00:00",
"samples": [
{
"@id": "/in-vitro-systems/IGVFSM1989ECAN/",
"@type": [
"InVitroSystem",
"Biosample",
"Sample",
"Item"
],
"accession": "IGVFSM1989ECAN",
"aliases": [
"jesse-engreitz:220228_8merInsertion-THP1-Amp_PPIF_promoter-BioRep1-FFrep3-BinE"
],
"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 80-90% 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": "2023-12-05T18:26:47.833520+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": "9187f03f-4661-450f-9828-70a131c67a0f"
}