{
"@context": "/terms/",
"@id": "/measurement-sets/IGVFDS2443IKFM/",
"@type": [
"MeasurementSet",
"FileSet",
"Item"
],
"accession": "IGVFDS2443IKFM",
"aliases": [
"jesse-engreitz:220228_8merInsertion-THP1-Amp_PPIF_promoter-BioRep4-FFrep2-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 [IGVFDS2443IKFM](/measurement-sets/IGVFDS2443IKFM/) 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/IGVFDS2443IKFM/"
},
{
"category": "missing sequencing kit",
"detail": "Measurement set [IGVFDS2443IKFM](/measurement-sets/IGVFDS2443IKFM/) has sequence file(s) [IGVFFI7144JIEE](/sequence-files/IGVFFI7144JIEE/), [IGVFFI9078JOPW](/sequence-files/IGVFFI9078JOPW/), [IGVFFI7132RPVS](/sequence-files/IGVFFI7132RPVS/), [IGVFFI7474NWFW](/sequence-files/IGVFFI7474NWFW/), [IGVFFI4395FBMH](/sequence-files/IGVFFI4395FBMH/), [IGVFFI6596UXNN](/sequence-files/IGVFFI6596UXNN/), [IGVFFI8402EJCS](/sequence-files/IGVFFI8402EJCS/), [IGVFFI8732THFQ](/sequence-files/IGVFFI8732THFQ/) 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/IGVFDS2443IKFM/"
},
{
"category": "missing sequence specification",
"detail": "Measurement set [IGVFDS2443IKFM](/measurement-sets/IGVFDS2443IKFM/) has sequence file(s): [IGVFFI7144JIEE](/sequence-files/IGVFFI7144JIEE/), [IGVFFI9078JOPW](/sequence-files/IGVFFI9078JOPW/), [IGVFFI7132RPVS](/sequence-files/IGVFFI7132RPVS/), [IGVFFI7474NWFW](/sequence-files/IGVFFI7474NWFW/), [IGVFFI4395FBMH](/sequence-files/IGVFFI4395FBMH/), [IGVFFI6596UXNN](/sequence-files/IGVFFI6596UXNN/), [IGVFFI8402EJCS](/sequence-files/IGVFFI8402EJCS/), [IGVFFI8732THFQ](/sequence-files/IGVFFI8732THFQ/) 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/IGVFDS2443IKFM/"
},
{
"category": "mismatched status",
"detail": "Released in vitro system [IGVFSM0787QFVT](/in-vitro-systems/IGVFSM0787QFVT/) 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/IGVFSM0787QFVT/"
},
{
"category": "missing publication",
"detail": "In vitro system [IGVFSM0787QFVT](/in-vitro-systems/IGVFSM0787QFVT/) 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/IGVFSM0787QFVT/"
}
],
"WARNING": [
{
"category": "missing auxiliary set",
"detail": "Measurement set [IGVFDS2443IKFM](/measurement-sets/IGVFDS2443IKFM/) 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/IGVFDS2443IKFM/"
}
]
},
"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": "2023-11-30T22:46:51.778478+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/IGVFFI7144JIEE/",
"accession": "IGVFFI7144JIEE",
"aliases": [
"jesse-engreitz:220228_8merInsertion-THP1-Amp_PPIF_promoter-BioRep4-FFrep2-BinE-PCRrep2_R2"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2023-12-05T18:52:48.273520+00:00",
"file_format": "fastq",
"file_size": 16992109,
"href": "/sequence-files/IGVFFI7144JIEE/@@download/IGVFFI7144JIEE.fastq.gz",
"s3_uri": "s3://igvf-files/2023/12/05/d3145db8-8251-4900-a1d2-a8068a878cc5/IGVFFI7144JIEE.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-BioRep2-FFRep2-BinE-PCRrep2_S129_R2_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI9078JOPW/",
"accession": "IGVFFI9078JOPW",
"aliases": [
"jesse-engreitz:220228_8merInsertion-THP1-Amp_PPIF_promoter-BioRep4-FFrep2-BinE-PCRrep2_R1"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2023-12-05T18:39:51.773254+00:00",
"file_format": "fastq",
"file_size": 8406962,
"href": "/sequence-files/IGVFFI9078JOPW/@@download/IGVFFI9078JOPW.fastq.gz",
"s3_uri": "s3://igvf-files/2023/12/05/29f96970-412b-444a-ba41-54c19fd9b279/IGVFFI9078JOPW.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-BioRep2-FFRep2-BinE-PCRrep2_S129_R1_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI7132RPVS/",
"accession": "IGVFFI7132RPVS",
"aliases": [
"jesse-engreitz:220228_8merInsertion-THP1-Amp_PPIF_promoter-BioRep4-FFrep2-BinE-PCRrep2_I2"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2023-12-05T19:17:36.268467+00:00",
"file_format": "fastq",
"file_size": 2902743,
"href": "/sequence-files/IGVFFI7132RPVS/@@download/IGVFFI7132RPVS.fastq.gz",
"s3_uri": "s3://igvf-files/2023/12/05/122c76be-989b-4be6-94c7-02668b3992e4/IGVFFI7132RPVS.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-BioRep2-FFRep2-BinE-PCRrep2_S129_I2_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI7474NWFW/",
"accession": "IGVFFI7474NWFW",
"aliases": [
"jesse-engreitz:220228_8merInsertion-THP1-Amp_PPIF_promoter-BioRep4-FFrep2-BinE-PCRrep2_I1"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2023-12-05T19:05:19.869004+00:00",
"file_format": "fastq",
"file_size": 3029280,
"href": "/sequence-files/IGVFFI7474NWFW/@@download/IGVFFI7474NWFW.fastq.gz",
"s3_uri": "s3://igvf-files/2023/12/05/39bab7b9-8be2-45cd-8e0d-0a51fdcb9b56/IGVFFI7474NWFW.fastq.gz",
"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-BioRep2-FFRep2-BinE-PCRrep2_S129_I1_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI4395FBMH/",
"accession": "IGVFFI4395FBMH",
"aliases": [
"jesse-engreitz:220228_8merInsertion-THP1-Amp_PPIF_promoter-BioRep4-FFrep2-BinE-PCRrep1_I2"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2023-12-05T19:11:29.646481+00:00",
"file_format": "fastq",
"file_size": 2802050,
"href": "/sequence-files/IGVFFI4395FBMH/@@download/IGVFFI4395FBMH.fastq.gz",
"s3_uri": "s3://igvf-files/2023/12/05/48976163-d6a8-4b89-b6d1-073b20a42b88/IGVFFI4395FBMH.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-BioRep2-FFRep2-BinE-PCRrep1_S33_I2_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI6596UXNN/",
"accession": "IGVFFI6596UXNN",
"aliases": [
"jesse-engreitz:220228_8merInsertion-THP1-Amp_PPIF_promoter-BioRep4-FFrep2-BinE-PCRrep1_R2"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2023-12-05T18:46:16.088390+00:00",
"file_format": "fastq",
"file_size": 16113987,
"href": "/sequence-files/IGVFFI6596UXNN/@@download/IGVFFI6596UXNN.fastq.gz",
"s3_uri": "s3://igvf-files/2023/12/05/f450b6d5-60d9-4549-a97b-569b69ac8fe5/IGVFFI6596UXNN.fastq.gz",
"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-BioRep2-FFRep2-BinE-PCRrep1_S33_R2_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI8402EJCS/",
"accession": "IGVFFI8402EJCS",
"aliases": [
"jesse-engreitz:220228_8merInsertion-THP1-Amp_PPIF_promoter-BioRep4-FFrep2-BinE-PCRrep1_I1"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2023-12-05T18:59:03.912245+00:00",
"file_format": "fastq",
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"s3_uri": "s3://igvf-files/2023/12/05/f13920d4-4375-483e-9501-2fdc09976971/IGVFFI8402EJCS.fastq.gz",
"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-BioRep2-FFRep2-BinE-PCRrep1_S33_I1_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI8732THFQ/",
"accession": "IGVFFI8732THFQ",
"aliases": [
"jesse-engreitz:220228_8merInsertion-THP1-Amp_PPIF_promoter-BioRep4-FFrep2-BinE-PCRrep1_R1"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2023-12-05T18:33:35.858194+00:00",
"file_format": "fastq",
"file_size": 8300646,
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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-BioRep2-FFRep2-BinE-PCRrep1_S33_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": "2023-12-20T23:09:27.503540+00:00",
"samples": [
{
"@id": "/in-vitro-systems/IGVFSM0787QFVT/",
"@type": [
"InVitroSystem",
"Biosample",
"Sample",
"Item"
],
"accession": "IGVFSM0787QFVT",
"aliases": [
"jesse-engreitz:220228_8merInsertion-THP1-Amp_PPIF_promoter-BioRep4-FFrep2-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": "2023-12-05T18:33:35.858194+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": "c64d7c63-1e88-4b8f-abc2-e764dcb328da"
}