{
"@context": "/terms/",
"@id": "/measurement-sets/IGVFDS6880HZFB/",
"@type": [
"MeasurementSet",
"FileSet",
"Item"
],
"accession": "IGVFDS6880HZFB",
"aliases": [
"jesse-engreitz:220228_8merInsertion-THP1-Amp_PPIF_promoter-BioRep3-FFrep2-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 [IGVFDS6880HZFB](/measurement-sets/IGVFDS6880HZFB/) 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/IGVFDS6880HZFB/"
},
{
"category": "missing sequencing kit",
"detail": "Measurement set [IGVFDS6880HZFB](/measurement-sets/IGVFDS6880HZFB/) has sequence file(s) [IGVFFI3740BMLM](/sequence-files/IGVFFI3740BMLM/), [IGVFFI8748THZZ](/sequence-files/IGVFFI8748THZZ/), [IGVFFI8757FHIP](/sequence-files/IGVFFI8757FHIP/), [IGVFFI8640ANUC](/sequence-files/IGVFFI8640ANUC/), [IGVFFI8318KIYP](/sequence-files/IGVFFI8318KIYP/), [IGVFFI6346QCWJ](/sequence-files/IGVFFI6346QCWJ/), [IGVFFI1351PMFJ](/sequence-files/IGVFFI1351PMFJ/), [IGVFFI4896HQUI](/sequence-files/IGVFFI4896HQUI/) 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/IGVFDS6880HZFB/"
},
{
"category": "missing sequence specification",
"detail": "Measurement set [IGVFDS6880HZFB](/measurement-sets/IGVFDS6880HZFB/) has sequence file(s): [IGVFFI3740BMLM](/sequence-files/IGVFFI3740BMLM/), [IGVFFI8748THZZ](/sequence-files/IGVFFI8748THZZ/), [IGVFFI8757FHIP](/sequence-files/IGVFFI8757FHIP/), [IGVFFI8640ANUC](/sequence-files/IGVFFI8640ANUC/), [IGVFFI8318KIYP](/sequence-files/IGVFFI8318KIYP/), [IGVFFI6346QCWJ](/sequence-files/IGVFFI6346QCWJ/), [IGVFFI1351PMFJ](/sequence-files/IGVFFI1351PMFJ/), [IGVFFI4896HQUI](/sequence-files/IGVFFI4896HQUI/) 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/IGVFDS6880HZFB/"
},
{
"category": "mismatched status",
"detail": "Released in vitro system [IGVFSM3062EIHZ](/in-vitro-systems/IGVFSM3062EIHZ/) 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/IGVFSM3062EIHZ/"
},
{
"category": "missing publication",
"detail": "In vitro system [IGVFSM3062EIHZ](/in-vitro-systems/IGVFSM3062EIHZ/) 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/IGVFSM3062EIHZ/"
}
],
"WARNING": [
{
"category": "missing auxiliary set",
"detail": "Measurement set [IGVFDS6880HZFB](/measurement-sets/IGVFDS6880HZFB/) 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/IGVFDS6880HZFB/"
}
]
},
"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": "2023-11-30T22:46:33.013653+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/IGVFFI3740BMLM/",
"accession": "IGVFFI3740BMLM",
"aliases": [
"jesse-engreitz:220228_8merInsertion-THP1-Amp_PPIF_promoter-BioRep3-FFrep2-BinD-PCRrep1_I2"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2023-12-05T19:08:13.732175+00:00",
"file_format": "fastq",
"file_size": 2666188,
"href": "/sequence-files/IGVFFI3740BMLM/@@download/IGVFFI3740BMLM.fastq.gz",
"s3_uri": "s3://igvf-files/2023/12/05/997bbbf7-3c34-4526-b094-25998e8d0a82/IGVFFI3740BMLM.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-FFRep2-BinD-PCRrep1_S11_I2_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI8748THZZ/",
"accession": "IGVFFI8748THZZ",
"aliases": [
"jesse-engreitz:220228_8merInsertion-THP1-Amp_PPIF_promoter-BioRep3-FFrep2-BinD-PCRrep1_R1"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2023-12-05T18:30:14.980606+00:00",
"file_format": "fastq",
"file_size": 7915052,
"href": "/sequence-files/IGVFFI8748THZZ/@@download/IGVFFI8748THZZ.fastq.gz",
"s3_uri": "s3://igvf-files/2023/12/05/a7cefd93-403b-4d1b-bb6b-1db3f4626875/IGVFFI8748THZZ.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-FFRep2-BinD-PCRrep1_S11_R1_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI8757FHIP/",
"accession": "IGVFFI8757FHIP",
"aliases": [
"jesse-engreitz:220228_8merInsertion-THP1-Amp_PPIF_promoter-BioRep3-FFrep2-BinD-PCRrep1_I1"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2023-12-05T18:55:46.442713+00:00",
"file_format": "fastq",
"file_size": 2802404,
"href": "/sequence-files/IGVFFI8757FHIP/@@download/IGVFFI8757FHIP.fastq.gz",
"s3_uri": "s3://igvf-files/2023/12/05/f5ade85a-9b03-4dbe-b84e-79d8c73b276b/IGVFFI8757FHIP.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-FFRep2-BinD-PCRrep1_S11_I1_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI8640ANUC/",
"accession": "IGVFFI8640ANUC",
"aliases": [
"jesse-engreitz:220228_8merInsertion-THP1-Amp_PPIF_promoter-BioRep3-FFrep2-BinD-PCRrep2_I1"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2023-12-05T19:02:09.991351+00:00",
"file_format": "fastq",
"file_size": 2898947,
"href": "/sequence-files/IGVFFI8640ANUC/@@download/IGVFFI8640ANUC.fastq.gz",
"s3_uri": "s3://igvf-files/2023/12/05/bee0374b-89d5-4023-98e6-e27aa6dbcbc1/IGVFFI8640ANUC.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-FFRep2-BinD-PCRrep2_S107_I1_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI8318KIYP/",
"accession": "IGVFFI8318KIYP",
"aliases": [
"jesse-engreitz:220228_8merInsertion-THP1-Amp_PPIF_promoter-BioRep3-FFrep2-BinD-PCRrep2_R2"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2023-12-05T18:49:19.203459+00:00",
"file_format": "fastq",
"file_size": 16144130,
"href": "/sequence-files/IGVFFI8318KIYP/@@download/IGVFFI8318KIYP.fastq.gz",
"s3_uri": "s3://igvf-files/2023/12/05/203dba52-4be2-4005-b088-0133ec32af82/IGVFFI8318KIYP.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-FFRep2-BinD-PCRrep2_S107_R2_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI6346QCWJ/",
"accession": "IGVFFI6346QCWJ",
"aliases": [
"jesse-engreitz:220228_8merInsertion-THP1-Amp_PPIF_promoter-BioRep3-FFrep2-BinD-PCRrep1_R2"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2023-12-05T18:42:54.794526+00:00",
"file_format": "fastq",
"file_size": 15360903,
"href": "/sequence-files/IGVFFI6346QCWJ/@@download/IGVFFI6346QCWJ.fastq.gz",
"s3_uri": "s3://igvf-files/2023/12/05/19a08b59-a19d-40ba-84c4-9c4da41efcee/IGVFFI6346QCWJ.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-FFRep2-BinD-PCRrep1_S11_R2_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI1351PMFJ/",
"accession": "IGVFFI1351PMFJ",
"aliases": [
"jesse-engreitz:220228_8merInsertion-THP1-Amp_PPIF_promoter-BioRep3-FFrep2-BinD-PCRrep2_I2"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2023-12-05T19:14:23.793802+00:00",
"file_format": "fastq",
"file_size": 2772288,
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"status": "released",
"term_name": "Illumina NextSeq 550"
},
"status": "released",
"submitted_file_name": "220426pPPIF_REPEAT-THP1-Gen8b-pPPIF-Amp_pPPIF-BioRep1-FFRep2-BinD-PCRrep2_S107_I2_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI4896HQUI/",
"accession": "IGVFFI4896HQUI",
"aliases": [
"jesse-engreitz:220228_8merInsertion-THP1-Amp_PPIF_promoter-BioRep3-FFrep2-BinD-PCRrep2_R1"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2023-12-05T18:36:33.779533+00:00",
"file_format": "fastq",
"file_size": 8059656,
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"sequencing_platform": {
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"status": "released",
"term_name": "Illumina NextSeq 550"
},
"status": "released",
"submitted_file_name": "220426pPPIF_REPEAT-THP1-Gen8b-pPPIF-Amp_pPPIF-BioRep1-FFRep2-BinD-PCRrep2_S107_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": "2023-12-20T23:10:52.107019+00:00",
"samples": [
{
"@id": "/in-vitro-systems/IGVFSM3062EIHZ/",
"@type": [
"InVitroSystem",
"Biosample",
"Sample",
"Item"
],
"accession": "IGVFSM3062EIHZ",
"aliases": [
"jesse-engreitz:220228_8merInsertion-THP1-Amp_PPIF_promoter-BioRep3-FFrep2-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": "2023-12-05T18:30:14.980606+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": "6a2429bb-28e2-4d64-9e7e-53b002f08f80"
}