{
"@context": "/terms/",
"@id": "/measurement-sets/IGVFDS4945KDNO/",
"@type": [
"MeasurementSet",
"FileSet",
"Item"
],
"accession": "IGVFDS4945KDNO",
"aliases": [
"jesse-engreitz:220228_8merInsertion-THP1-Amp_PPIF_promoter-BioRep1-FFrep1-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 [IGVFDS4945KDNO](/measurement-sets/IGVFDS4945KDNO/) 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/IGVFDS4945KDNO/"
},
{
"category": "missing sequencing kit",
"detail": "Measurement set [IGVFDS4945KDNO](/measurement-sets/IGVFDS4945KDNO/) has sequence file(s) [IGVFFI1365OBNL](/sequence-files/IGVFFI1365OBNL/), [IGVFFI8071KRUC](/sequence-files/IGVFFI8071KRUC/), [IGVFFI0797HVIK](/sequence-files/IGVFFI0797HVIK/), [IGVFFI7398IHGE](/sequence-files/IGVFFI7398IHGE/), [IGVFFI7923HFPY](/sequence-files/IGVFFI7923HFPY/), [IGVFFI2897OQBO](/sequence-files/IGVFFI2897OQBO/), [IGVFFI4818DUQU](/sequence-files/IGVFFI4818DUQU/), [IGVFFI7430XNHQ](/sequence-files/IGVFFI7430XNHQ/) 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/IGVFDS4945KDNO/"
},
{
"category": "missing sequence specification",
"detail": "Measurement set [IGVFDS4945KDNO](/measurement-sets/IGVFDS4945KDNO/) has sequence file(s): [IGVFFI1365OBNL](/sequence-files/IGVFFI1365OBNL/), [IGVFFI8071KRUC](/sequence-files/IGVFFI8071KRUC/), [IGVFFI0797HVIK](/sequence-files/IGVFFI0797HVIK/), [IGVFFI7398IHGE](/sequence-files/IGVFFI7398IHGE/), [IGVFFI7923HFPY](/sequence-files/IGVFFI7923HFPY/), [IGVFFI2897OQBO](/sequence-files/IGVFFI2897OQBO/), [IGVFFI4818DUQU](/sequence-files/IGVFFI4818DUQU/), [IGVFFI7430XNHQ](/sequence-files/IGVFFI7430XNHQ/) 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/IGVFDS4945KDNO/"
},
{
"category": "mismatched status",
"detail": "Released in vitro system [IGVFSM9821UQTT](/in-vitro-systems/IGVFSM9821UQTT/) 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/IGVFSM9821UQTT/"
},
{
"category": "missing publication",
"detail": "In vitro system [IGVFSM9821UQTT](/in-vitro-systems/IGVFSM9821UQTT/) 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/IGVFSM9821UQTT/"
}
],
"WARNING": [
{
"category": "missing auxiliary set",
"detail": "Measurement set [IGVFDS4945KDNO](/measurement-sets/IGVFDS4945KDNO/) 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/IGVFDS4945KDNO/"
}
]
},
"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": "2023-12-01T00:01:47.907686+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/IGVFFI1365OBNL/",
"accession": "IGVFFI1365OBNL",
"aliases": [
"jesse-engreitz:220228_8merInsertion-THP1-Amp_PPIF_promoter-BioRep1-FFrep1-BinE-PCRrep1_I2"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2023-12-05T18:59:15.701119+00:00",
"file_format": "fastq",
"file_size": 14251905,
"href": "/sequence-files/IGVFFI1365OBNL/@@download/IGVFFI1365OBNL.fastq.gz",
"s3_uri": "s3://igvf-files/2023/12/05/de713700-a299-49ed-8b6e-eb8de8a7eb8b/IGVFFI1365OBNL.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-BinE_I2_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI8071KRUC/",
"accession": "IGVFFI8071KRUC",
"aliases": [
"jesse-engreitz:220228_8merInsertion-THP1-Amp_PPIF_promoter-BioRep1-FFrep1-BinE-PCRrep1_R2"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2023-12-05T18:36:05.465386+00:00",
"file_format": "fastq",
"file_size": 74828483,
"href": "/sequence-files/IGVFFI8071KRUC/@@download/IGVFFI8071KRUC.fastq.gz",
"s3_uri": "s3://igvf-files/2023/12/05/84ac2937-92a0-4fcf-bd3d-9ca85c771363/IGVFFI8071KRUC.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-BinE_R2_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI0797HVIK/",
"accession": "IGVFFI0797HVIK",
"aliases": [
"jesse-engreitz:220228_8merInsertion-THP1-Amp_PPIF_promoter-BioRep1-FFrep1-BinE-PCRrep2_I1"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2023-12-05T18:53:35.973570+00:00",
"file_format": "fastq",
"file_size": 15152323,
"href": "/sequence-files/IGVFFI0797HVIK/@@download/IGVFFI0797HVIK.fastq.gz",
"s3_uri": "s3://igvf-files/2023/12/05/bbd873aa-18f9-4c8a-9d25-69061540e384/IGVFFI0797HVIK.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-BinE_I1_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI7398IHGE/",
"accession": "IGVFFI7398IHGE",
"aliases": [
"jesse-engreitz:220228_8merInsertion-THP1-Amp_PPIF_promoter-BioRep1-FFrep1-BinE-PCRrep2_R2"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2023-12-05T18:42:08.344890+00:00",
"file_format": "fastq",
"file_size": 72779758,
"href": "/sequence-files/IGVFFI7398IHGE/@@download/IGVFFI7398IHGE.fastq.gz",
"s3_uri": "s3://igvf-files/2023/12/05/8be070bb-eb83-44e3-8f2e-4b51f30eec30/IGVFFI7398IHGE.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-BinE_R2_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI7923HFPY/",
"accession": "IGVFFI7923HFPY",
"aliases": [
"jesse-engreitz:220228_8merInsertion-THP1-Amp_PPIF_promoter-BioRep1-FFrep1-BinE-PCRrep1_R1"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2023-12-05T18:24:37.493307+00:00",
"file_format": "fastq",
"file_size": 41648218,
"href": "/sequence-files/IGVFFI7923HFPY/@@download/IGVFFI7923HFPY.fastq.gz",
"s3_uri": "s3://igvf-files/2023/12/05/2b6f8745-7044-4459-87aa-c27f732d0c79/IGVFFI7923HFPY.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-BinE_R1_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI2897OQBO/",
"accession": "IGVFFI2897OQBO",
"aliases": [
"jesse-engreitz:220228_8merInsertion-THP1-Amp_PPIF_promoter-BioRep1-FFrep1-BinE-PCRrep2_R1"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2023-12-05T18:30:20.746215+00:00",
"file_format": "fastq",
"file_size": 40573773,
"href": "/sequence-files/IGVFFI2897OQBO/@@download/IGVFFI2897OQBO.fastq.gz",
"s3_uri": "s3://igvf-files/2023/12/05/6e1909ba-ede7-4e29-89d8-7c3866dded6d/IGVFFI2897OQBO.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-BinE_R1_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI4818DUQU/",
"accession": "IGVFFI4818DUQU",
"aliases": [
"jesse-engreitz:220228_8merInsertion-THP1-Amp_PPIF_promoter-BioRep1-FFrep1-BinE-PCRrep2_I2"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2023-12-05T19:04:47.783585+00:00",
"file_format": "fastq",
"file_size": 13836616,
"href": "/sequence-files/IGVFFI4818DUQU/@@download/IGVFFI4818DUQU.fastq.gz",
"s3_uri": "s3://igvf-files/2023/12/05/f28e63cd-fd8e-4878-aa95-1d055d144cbf/IGVFFI4818DUQU.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-BinE_I2_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI7430XNHQ/",
"accession": "IGVFFI7430XNHQ",
"aliases": [
"jesse-engreitz:220228_8merInsertion-THP1-Amp_PPIF_promoter-BioRep1-FFrep1-BinE-PCRrep1_I1"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2023-12-05T18:48:02.897944+00:00",
"file_format": "fastq",
"file_size": 15143278,
"href": "/sequence-files/IGVFFI7430XNHQ/@@download/IGVFFI7430XNHQ.fastq.gz",
"s3_uri": "s3://igvf-files/2023/12/05/38e1d7dc-644f-4bd4-bb9d-c277b5d5933b/IGVFFI7430XNHQ.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-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": "2023-12-20T23:09:15.432123+00:00",
"samples": [
{
"@id": "/in-vitro-systems/IGVFSM9821UQTT/",
"@type": [
"InVitroSystem",
"Biosample",
"Sample",
"Item"
],
"accession": "IGVFSM9821UQTT",
"aliases": [
"jesse-engreitz:220228_8merInsertion-THP1-Amp_PPIF_promoter-BioRep1-FFrep1-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": "2023-12-05T18:24:37.493307+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": "0ebf578b-e286-417f-bb77-3dd11ffb1d00"
}