{
"@context": "/terms/",
"@id": "/measurement-sets/IGVFDS5961WERM/",
"@type": [
"MeasurementSet",
"FileSet",
"Item"
],
"accession": "IGVFDS5961WERM",
"aliases": [
"jesse-engreitz:220228_8merInsertion-THP1-Amp_PPIF_promoter-BioRep3-FFrep3-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": "mismatched status",
"detail": "Released in vitro system [IGVFSM0595JWOO](/in-vitro-systems/IGVFSM0595JWOO/) 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/IGVFSM0595JWOO/"
},
{
"category": "missing publication",
"detail": "In vitro system [IGVFSM0595JWOO](/in-vitro-systems/IGVFSM0595JWOO/) 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/IGVFSM0595JWOO/"
},
{
"category": "missing publication",
"detail": "Measurement set [IGVFDS5961WERM](/measurement-sets/IGVFDS5961WERM/) 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/IGVFDS5961WERM/"
},
{
"category": "missing sequencing kit",
"detail": "Measurement set [IGVFDS5961WERM](/measurement-sets/IGVFDS5961WERM/) has sequence file(s) [IGVFFI1141ZGFP](/sequence-files/IGVFFI1141ZGFP/), [IGVFFI7945BUST](/sequence-files/IGVFFI7945BUST/), [IGVFFI6597LAWS](/sequence-files/IGVFFI6597LAWS/), [IGVFFI1044LIFI](/sequence-files/IGVFFI1044LIFI/), [IGVFFI1731ACNS](/sequence-files/IGVFFI1731ACNS/), [IGVFFI2122WBEB](/sequence-files/IGVFFI2122WBEB/), [IGVFFI7652TITI](/sequence-files/IGVFFI7652TITI/), [IGVFFI8567OKOG](/sequence-files/IGVFFI8567OKOG/) 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/IGVFDS5961WERM/"
},
{
"category": "missing sequence specification",
"detail": "Measurement set [IGVFDS5961WERM](/measurement-sets/IGVFDS5961WERM/) has sequence file(s): [IGVFFI1141ZGFP](/sequence-files/IGVFFI1141ZGFP/), [IGVFFI7945BUST](/sequence-files/IGVFFI7945BUST/), [IGVFFI6597LAWS](/sequence-files/IGVFFI6597LAWS/), [IGVFFI1044LIFI](/sequence-files/IGVFFI1044LIFI/), [IGVFFI1731ACNS](/sequence-files/IGVFFI1731ACNS/), [IGVFFI2122WBEB](/sequence-files/IGVFFI2122WBEB/), [IGVFFI7652TITI](/sequence-files/IGVFFI7652TITI/), [IGVFFI8567OKOG](/sequence-files/IGVFFI8567OKOG/) 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/IGVFDS5961WERM/"
}
],
"WARNING": [
{
"category": "missing auxiliary set",
"detail": "Measurement set [IGVFDS5961WERM](/measurement-sets/IGVFDS5961WERM/) 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/IGVFDS5961WERM/"
}
]
},
"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": "2023-11-30T22:46:39.222445+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/IGVFFI1141ZGFP/",
"accession": "IGVFFI1141ZGFP",
"aliases": [
"jesse-engreitz:220228_8merInsertion-THP1-Amp_PPIF_promoter-BioRep3-FFrep3-BinD-PCRrep1_I1"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2023-12-05T18:56:48.531377+00:00",
"file_format": "fastq",
"file_size": 2863303,
"href": "/sequence-files/IGVFFI1141ZGFP/@@download/IGVFFI1141ZGFP.fastq.gz",
"s3_uri": "s3://igvf-files/2023/12/05/08b979f8-bbd2-4e77-bdab-eb8f4e5d4868/IGVFFI1141ZGFP.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-FFRep3-BinD-PCRrep1_S18_I1_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI7945BUST/",
"accession": "IGVFFI7945BUST",
"aliases": [
"jesse-engreitz:220228_8merInsertion-THP1-Amp_PPIF_promoter-BioRep3-FFrep3-BinD-PCRrep2_I2"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2023-12-05T19:15:25.307156+00:00",
"file_format": "fastq",
"file_size": 2764541,
"href": "/sequence-files/IGVFFI7945BUST/@@download/IGVFFI7945BUST.fastq.gz",
"s3_uri": "s3://igvf-files/2023/12/05/3737defd-422b-485a-bc01-08bd2ad4145f/IGVFFI7945BUST.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-FFRep3-BinD-PCRrep2_S114_I2_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI6597LAWS/",
"accession": "IGVFFI6597LAWS",
"aliases": [
"jesse-engreitz:220228_8merInsertion-THP1-Amp_PPIF_promoter-BioRep3-FFrep3-BinD-PCRrep1_R1"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2023-12-05T18:31:17.887094+00:00",
"file_format": "fastq",
"file_size": 7949923,
"href": "/sequence-files/IGVFFI6597LAWS/@@download/IGVFFI6597LAWS.fastq.gz",
"s3_uri": "s3://igvf-files/2023/12/05/5307e94d-e3b8-48a6-8e58-9a59a3eb0f18/IGVFFI6597LAWS.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-FFRep3-BinD-PCRrep1_S18_R1_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI1044LIFI/",
"accession": "IGVFFI1044LIFI",
"aliases": [
"jesse-engreitz:220228_8merInsertion-THP1-Amp_PPIF_promoter-BioRep3-FFrep3-BinD-PCRrep2_I1"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2023-12-05T19:03:10.135626+00:00",
"file_format": "fastq",
"file_size": 2906341,
"href": "/sequence-files/IGVFFI1044LIFI/@@download/IGVFFI1044LIFI.fastq.gz",
"s3_uri": "s3://igvf-files/2023/12/05/fbe3b691-0353-4523-9175-3c84a5a69d3f/IGVFFI1044LIFI.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-FFRep3-BinD-PCRrep2_S114_I1_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI1731ACNS/",
"accession": "IGVFFI1731ACNS",
"aliases": [
"jesse-engreitz:220228_8merInsertion-THP1-Amp_PPIF_promoter-BioRep3-FFrep3-BinD-PCRrep1_I2"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2023-12-05T19:09:14.592777+00:00",
"file_format": "fastq",
"file_size": 2701360,
"href": "/sequence-files/IGVFFI1731ACNS/@@download/IGVFFI1731ACNS.fastq.gz",
"s3_uri": "s3://igvf-files/2023/12/05/c2d234b8-95a1-4dd2-bac1-3bc375399db9/IGVFFI1731ACNS.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-FFRep3-BinD-PCRrep1_S18_I2_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI2122WBEB/",
"accession": "IGVFFI2122WBEB",
"aliases": [
"jesse-engreitz:220228_8merInsertion-THP1-Amp_PPIF_promoter-BioRep3-FFrep3-BinD-PCRrep1_R2"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2023-12-05T18:43:58.738709+00:00",
"file_format": "fastq",
"file_size": 15691861,
"href": "/sequence-files/IGVFFI2122WBEB/@@download/IGVFFI2122WBEB.fastq.gz",
"s3_uri": "s3://igvf-files/2023/12/05/e0966af6-ec14-46b6-8206-ef2e133885fb/IGVFFI2122WBEB.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-FFRep3-BinD-PCRrep1_S18_R2_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI7652TITI/",
"accession": "IGVFFI7652TITI",
"aliases": [
"jesse-engreitz:220228_8merInsertion-THP1-Amp_PPIF_promoter-BioRep3-FFrep3-BinD-PCRrep2_R2"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2023-12-05T18:50:23.499509+00:00",
"file_format": "fastq",
"file_size": 16540070,
"href": "/sequence-files/IGVFFI7652TITI/@@download/IGVFFI7652TITI.fastq.gz",
"s3_uri": "s3://igvf-files/2023/12/05/9f0f49b8-1131-46c7-b435-e99a0ca53aa2/IGVFFI7652TITI.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-FFRep3-BinD-PCRrep2_S114_R2_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI8567OKOG/",
"accession": "IGVFFI8567OKOG",
"aliases": [
"jesse-engreitz:220228_8merInsertion-THP1-Amp_PPIF_promoter-BioRep3-FFrep3-BinD-PCRrep2_R1"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2023-12-05T18:37:37.023317+00:00",
"file_format": "fastq",
"file_size": 8009216,
"href": "/sequence-files/IGVFFI8567OKOG/@@download/IGVFFI8567OKOG.fastq.gz",
"s3_uri": "s3://igvf-files/2023/12/05/3e52479c-7f14-4f36-b8eb-44679e266946/IGVFFI8567OKOG.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-FFRep3-BinD-PCRrep2_S114_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": "2023-12-20T23:11:12.293288+00:00",
"samples": [
{
"@id": "/in-vitro-systems/IGVFSM0595JWOO/",
"@type": [
"InVitroSystem",
"Biosample",
"Sample",
"Item"
],
"accession": "IGVFSM0595JWOO",
"aliases": [
"jesse-engreitz:220228_8merInsertion-THP1-Amp_PPIF_promoter-BioRep3-FFrep3-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": "2023-12-05T18:31:17.887094+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": "91afff67-658f-4631-b429-980ce970f393"
}