{
"@context": "/terms/",
"@id": "/measurement-sets/IGVFDS0634BYKS/",
"@type": [
"MeasurementSet",
"FileSet",
"Item"
],
"accession": "IGVFDS0634BYKS",
"aliases": [
"jesse-engreitz:220228_8merInsertion-THP1-Amp_PPIF_promoter-BioRep3-FFrep1-BinD_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 [IGVFDS0634BYKS](/measurement-sets/IGVFDS0634BYKS/) 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/IGVFDS0634BYKS/"
},
{
"category": "missing sequencing kit",
"detail": "Measurement set [IGVFDS0634BYKS](/measurement-sets/IGVFDS0634BYKS/) has sequence file(s) [IGVFFI5732GWVX](/sequence-files/IGVFFI5732GWVX/), [IGVFFI8548IENT](/sequence-files/IGVFFI8548IENT/), [IGVFFI4637ORLS](/sequence-files/IGVFFI4637ORLS/), [IGVFFI3092JDSK](/sequence-files/IGVFFI3092JDSK/), [IGVFFI3430EIDL](/sequence-files/IGVFFI3430EIDL/), [IGVFFI3894YODL](/sequence-files/IGVFFI3894YODL/), [IGVFFI6059VDZF](/sequence-files/IGVFFI6059VDZF/), [IGVFFI0145LPCE](/sequence-files/IGVFFI0145LPCE/) 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/IGVFDS0634BYKS/"
},
{
"category": "missing sequence specification",
"detail": "Measurement set [IGVFDS0634BYKS](/measurement-sets/IGVFDS0634BYKS/) has sequence file(s): [IGVFFI5732GWVX](/sequence-files/IGVFFI5732GWVX/), [IGVFFI8548IENT](/sequence-files/IGVFFI8548IENT/), [IGVFFI4637ORLS](/sequence-files/IGVFFI4637ORLS/), [IGVFFI3092JDSK](/sequence-files/IGVFFI3092JDSK/), [IGVFFI3430EIDL](/sequence-files/IGVFFI3430EIDL/), [IGVFFI3894YODL](/sequence-files/IGVFFI3894YODL/), [IGVFFI6059VDZF](/sequence-files/IGVFFI6059VDZF/), [IGVFFI0145LPCE](/sequence-files/IGVFFI0145LPCE/) 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/IGVFDS0634BYKS/"
},
{
"category": "mismatched status",
"detail": "Released in vitro system [IGVFSM0320EORI](/in-vitro-systems/IGVFSM0320EORI/) 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/IGVFSM0320EORI/"
},
{
"category": "missing publication",
"detail": "In vitro system [IGVFSM0320EORI](/in-vitro-systems/IGVFSM0320EORI/) 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/IGVFSM0320EORI/"
}
],
"WARNING": [
{
"category": "missing auxiliary set",
"detail": "Measurement set [IGVFDS0634BYKS](/measurement-sets/IGVFDS0634BYKS/) 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/IGVFDS0634BYKS/"
}
]
},
"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": "2023-11-30T22:46:26.901522+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/IGVFFI5732GWVX/",
"accession": "IGVFFI5732GWVX",
"aliases": [
"jesse-engreitz:220228_8merInsertion-THP1-Amp_PPIF_promoter-BioRep3-FFrep1-BinD-PCRrep2_I2"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2023-12-05T19:13:22.795238+00:00",
"file_format": "fastq",
"file_size": 2365960,
"href": "/sequence-files/IGVFFI5732GWVX/@@download/IGVFFI5732GWVX.fastq.gz",
"s3_uri": "s3://igvf-files/2023/12/05/d63b95df-4ad9-407a-a7d4-6e13e377d0b2/IGVFFI5732GWVX.fastq.gz",
"sequencing_platform": {
"@id": "/platform-terms/EFO_0008566/",
"status": "released",
"term_name": "Illumina NextSeq 550"
},
"status": "released",
"submitted_file_name": "220426pPPIF_REPEAT-THP1-Gen8b-pPPIF-Amp_pPPIF-BioRep1-FFRep1-BinD-PCRrep2_S100_I2_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI8548IENT/",
"accession": "IGVFFI8548IENT",
"aliases": [
"jesse-engreitz:220228_8merInsertion-THP1-Amp_PPIF_promoter-BioRep3-FFrep1-BinD-PCRrep1_R1"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2023-12-05T18:29:11.756447+00:00",
"file_format": "fastq",
"file_size": 6878171,
"href": "/sequence-files/IGVFFI8548IENT/@@download/IGVFFI8548IENT.fastq.gz",
"s3_uri": "s3://igvf-files/2023/12/05/cc607f10-d2f9-4dee-8eb0-207b2761707e/IGVFFI8548IENT.fastq.gz",
"sequencing_platform": {
"@id": "/platform-terms/EFO_0008566/",
"status": "released",
"term_name": "Illumina NextSeq 550"
},
"status": "released",
"submitted_file_name": "220426pPPIF_REPEAT-THP1-Gen8b-pPPIF-Amp_pPPIF-BioRep1-FFRep1-BinD-PCRrep1_S4_R1_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI4637ORLS/",
"accession": "IGVFFI4637ORLS",
"aliases": [
"jesse-engreitz:220228_8merInsertion-THP1-Amp_PPIF_promoter-BioRep3-FFrep1-BinD-PCRrep1_I2"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2023-12-05T19:07:12.995550+00:00",
"file_format": "fastq",
"file_size": 2339189,
"href": "/sequence-files/IGVFFI4637ORLS/@@download/IGVFFI4637ORLS.fastq.gz",
"s3_uri": "s3://igvf-files/2023/12/05/92c43b57-e8e1-4fb6-95a4-0c2d9730f549/IGVFFI4637ORLS.fastq.gz",
"sequencing_platform": {
"@id": "/platform-terms/EFO_0008566/",
"status": "released",
"term_name": "Illumina NextSeq 550"
},
"status": "released",
"submitted_file_name": "220426pPPIF_REPEAT-THP1-Gen8b-pPPIF-Amp_pPPIF-BioRep1-FFRep1-BinD-PCRrep1_S4_I2_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI3092JDSK/",
"accession": "IGVFFI3092JDSK",
"aliases": [
"jesse-engreitz:220228_8merInsertion-THP1-Amp_PPIF_promoter-BioRep3-FFrep1-BinD-PCRrep2_I1"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2023-12-05T19:01:05.434481+00:00",
"file_format": "fastq",
"file_size": 2448731,
"href": "/sequence-files/IGVFFI3092JDSK/@@download/IGVFFI3092JDSK.fastq.gz",
"s3_uri": "s3://igvf-files/2023/12/05/454e515d-542f-4b04-9ec6-8ecc263987c0/IGVFFI3092JDSK.fastq.gz",
"sequencing_platform": {
"@id": "/platform-terms/EFO_0008566/",
"status": "released",
"term_name": "Illumina NextSeq 550"
},
"status": "released",
"submitted_file_name": "220426pPPIF_REPEAT-THP1-Gen8b-pPPIF-Amp_pPPIF-BioRep1-FFRep1-BinD-PCRrep2_S100_I1_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI3430EIDL/",
"accession": "IGVFFI3430EIDL",
"aliases": [
"jesse-engreitz:220228_8merInsertion-THP1-Amp_PPIF_promoter-BioRep3-FFrep1-BinD-PCRrep2_R2"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2023-12-05T18:48:15.080199+00:00",
"file_format": "fastq",
"file_size": 13379335,
"href": "/sequence-files/IGVFFI3430EIDL/@@download/IGVFFI3430EIDL.fastq.gz",
"s3_uri": "s3://igvf-files/2023/12/05/5ef5cf59-7c06-417b-9e45-710514d97f6f/IGVFFI3430EIDL.fastq.gz",
"sequencing_platform": {
"@id": "/platform-terms/EFO_0008566/",
"status": "released",
"term_name": "Illumina NextSeq 550"
},
"status": "released",
"submitted_file_name": "220426pPPIF_REPEAT-THP1-Gen8b-pPPIF-Amp_pPPIF-BioRep1-FFRep1-BinD-PCRrep2_S100_R2_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI3894YODL/",
"accession": "IGVFFI3894YODL",
"aliases": [
"jesse-engreitz:220228_8merInsertion-THP1-Amp_PPIF_promoter-BioRep3-FFrep1-BinD-PCRrep1_I1"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2023-12-05T18:54:45.523040+00:00",
"file_format": "fastq",
"file_size": 2443427,
"href": "/sequence-files/IGVFFI3894YODL/@@download/IGVFFI3894YODL.fastq.gz",
"s3_uri": "s3://igvf-files/2023/12/05/1284a744-9802-4e58-a2d2-4ff94ed24c0c/IGVFFI3894YODL.fastq.gz",
"sequencing_platform": {
"@id": "/platform-terms/EFO_0008566/",
"status": "released",
"term_name": "Illumina NextSeq 550"
},
"status": "released",
"submitted_file_name": "220426pPPIF_REPEAT-THP1-Gen8b-pPPIF-Amp_pPPIF-BioRep1-FFRep1-BinD-PCRrep1_S4_I1_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI6059VDZF/",
"accession": "IGVFFI6059VDZF",
"aliases": [
"jesse-engreitz:220228_8merInsertion-THP1-Amp_PPIF_promoter-BioRep3-FFrep1-BinD-PCRrep1_R2"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2023-12-05T18:41:50.443104+00:00",
"file_format": "fastq",
"file_size": 13279080,
"href": "/sequence-files/IGVFFI6059VDZF/@@download/IGVFFI6059VDZF.fastq.gz",
"s3_uri": "s3://igvf-files/2023/12/05/6e532fe1-3cf2-4b03-b24f-46c093a92317/IGVFFI6059VDZF.fastq.gz",
"sequencing_platform": {
"@id": "/platform-terms/EFO_0008566/",
"status": "released",
"term_name": "Illumina NextSeq 550"
},
"status": "released",
"submitted_file_name": "220426pPPIF_REPEAT-THP1-Gen8b-pPPIF-Amp_pPPIF-BioRep1-FFRep1-BinD-PCRrep1_S4_R2_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI0145LPCE/",
"accession": "IGVFFI0145LPCE",
"aliases": [
"jesse-engreitz:220228_8merInsertion-THP1-Amp_PPIF_promoter-BioRep3-FFrep1-BinD-PCRrep2_R1"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2023-12-05T18:35:31.895103+00:00",
"file_format": "fastq",
"file_size": 6820716,
"href": "/sequence-files/IGVFFI0145LPCE/@@download/IGVFFI0145LPCE.fastq.gz",
"s3_uri": "s3://igvf-files/2023/12/05/ecdc8b70-cbe5-4c74-be0b-0c4f93a1a6bf/IGVFFI0145LPCE.fastq.gz",
"sequencing_platform": {
"@id": "/platform-terms/EFO_0008566/",
"status": "released",
"term_name": "Illumina NextSeq 550"
},
"status": "released",
"submitted_file_name": "220426pPPIF_REPEAT-THP1-Gen8b-pPPIF-Amp_pPPIF-BioRep1-FFRep1-BinD-PCRrep2_S100_R1_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": "2023-12-20T23:09:33.307115+00:00",
"samples": [
{
"@id": "/in-vitro-systems/IGVFSM0320EORI/",
"@type": [
"InVitroSystem",
"Biosample",
"Sample",
"Item"
],
"accession": "IGVFSM0320EORI",
"aliases": [
"jesse-engreitz:220228_8merInsertion-THP1-Amp_PPIF_promoter-BioRep3-FFrep1-BinD"
],
"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 55-65% 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": "2023-12-05T18:29:11.756447+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": "ed871d7b-d56b-4b83-b9fc-e1c7957a8bc0"
}