{
"@context": "/terms/",
"@id": "/measurement-sets/IGVFDS4701EMZA/",
"@type": [
"MeasurementSet",
"FileSet",
"Item"
],
"accession": "IGVFDS4701EMZA",
"aliases": [
"jesse-engreitz:220228_8merInsertion-THP1-Amp_PPIF_promoter-BioRep4-FFrep1-BinF_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 [IGVFSM4555JSOF](/in-vitro-systems/IGVFSM4555JSOF/) 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/IGVFSM4555JSOF/"
},
{
"category": "missing publication",
"detail": "In vitro system [IGVFSM4555JSOF](/in-vitro-systems/IGVFSM4555JSOF/) 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/IGVFSM4555JSOF/"
},
{
"category": "missing publication",
"detail": "Measurement set [IGVFDS4701EMZA](/measurement-sets/IGVFDS4701EMZA/) 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/IGVFDS4701EMZA/"
},
{
"category": "missing sequencing kit",
"detail": "Measurement set [IGVFDS4701EMZA](/measurement-sets/IGVFDS4701EMZA/) has sequence file(s) [IGVFFI2667WHWJ](/sequence-files/IGVFFI2667WHWJ/), [IGVFFI5199YUFA](/sequence-files/IGVFFI5199YUFA/), [IGVFFI7752UHPV](/sequence-files/IGVFFI7752UHPV/), [IGVFFI6269LJOP](/sequence-files/IGVFFI6269LJOP/), [IGVFFI6480QWYG](/sequence-files/IGVFFI6480QWYG/), [IGVFFI7479XLVI](/sequence-files/IGVFFI7479XLVI/), [IGVFFI9569VGFF](/sequence-files/IGVFFI9569VGFF/), [IGVFFI6053TTFN](/sequence-files/IGVFFI6053TTFN/) 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/IGVFDS4701EMZA/"
},
{
"category": "missing sequence specification",
"detail": "Measurement set [IGVFDS4701EMZA](/measurement-sets/IGVFDS4701EMZA/) has sequence file(s): [IGVFFI2667WHWJ](/sequence-files/IGVFFI2667WHWJ/), [IGVFFI5199YUFA](/sequence-files/IGVFFI5199YUFA/), [IGVFFI7752UHPV](/sequence-files/IGVFFI7752UHPV/), [IGVFFI6269LJOP](/sequence-files/IGVFFI6269LJOP/), [IGVFFI6480QWYG](/sequence-files/IGVFFI6480QWYG/), [IGVFFI7479XLVI](/sequence-files/IGVFFI7479XLVI/), [IGVFFI9569VGFF](/sequence-files/IGVFFI9569VGFF/), [IGVFFI6053TTFN](/sequence-files/IGVFFI6053TTFN/) 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/IGVFDS4701EMZA/"
}
],
"WARNING": [
{
"category": "missing auxiliary set",
"detail": "Measurement set [IGVFDS4701EMZA](/measurement-sets/IGVFDS4701EMZA/) 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/IGVFDS4701EMZA/"
}
]
},
"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": "2023-11-30T22:46:46.825012+00:00",
"data_use_limitation_summaries": [
"no certificate"
],
"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/IGVFFI2667WHWJ/",
"accession": "IGVFFI2667WHWJ",
"aliases": [
"jesse-engreitz:220228_8merInsertion-THP1-Amp_PPIF_promoter-BioRep4-FFrep1-BinF-PCRrep1_R1"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2023-12-05T18:32:40.981762+00:00",
"file_format": "fastq",
"file_size": 7955778,
"href": "/sequence-files/IGVFFI2667WHWJ/@@download/IGVFFI2667WHWJ.fastq.gz",
"md5sum": "853525570dd297e5c04e39bb013ad1c2",
"s3_uri": "s3://igvf-files/2023/12/05/102b829b-d2a0-4e95-a9ad-423fff306a7f/IGVFFI2667WHWJ.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-FFRep1-BinF-PCRrep1_S27_R1_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI5199YUFA/",
"accession": "IGVFFI5199YUFA",
"aliases": [
"jesse-engreitz:220228_8merInsertion-THP1-Amp_PPIF_promoter-BioRep4-FFrep1-BinF-PCRrep1_I2"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2023-12-05T19:10:32.659050+00:00",
"file_format": "fastq",
"file_size": 2702417,
"href": "/sequence-files/IGVFFI5199YUFA/@@download/IGVFFI5199YUFA.fastq.gz",
"md5sum": "2c5cefe5cca1e49ef66b477ee2b89df5",
"s3_uri": "s3://igvf-files/2023/12/05/b3ba8994-032d-4609-8900-207862822350/IGVFFI5199YUFA.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-FFRep1-BinF-PCRrep1_S27_I2_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI7752UHPV/",
"accession": "IGVFFI7752UHPV",
"aliases": [
"jesse-engreitz:220228_8merInsertion-THP1-Amp_PPIF_promoter-BioRep4-FFrep1-BinF-PCRrep2_I1"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2023-12-05T19:04:28.480791+00:00",
"file_format": "fastq",
"file_size": 2856667,
"href": "/sequence-files/IGVFFI7752UHPV/@@download/IGVFFI7752UHPV.fastq.gz",
"md5sum": "c849b0e936c6baf04f2dbc31a5ce0f31",
"s3_uri": "s3://igvf-files/2023/12/05/3dc7e23d-5bb4-4345-ad5a-29bbed820e57/IGVFFI7752UHPV.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-FFRep1-BinF-PCRrep2_S123_I1_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI6269LJOP/",
"accession": "IGVFFI6269LJOP",
"aliases": [
"jesse-engreitz:220228_8merInsertion-THP1-Amp_PPIF_promoter-BioRep4-FFrep1-BinF-PCRrep1_I1"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2023-12-05T18:58:08.015070+00:00",
"file_format": "fastq",
"file_size": 2763971,
"href": "/sequence-files/IGVFFI6269LJOP/@@download/IGVFFI6269LJOP.fastq.gz",
"md5sum": "03d5fd5084dc921cd9a9e1f5649dbbf0",
"s3_uri": "s3://igvf-files/2023/12/05/d0539897-e012-4895-9845-80a0b6e25be6/IGVFFI6269LJOP.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-FFRep1-BinF-PCRrep1_S27_I1_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI6480QWYG/",
"accession": "IGVFFI6480QWYG",
"aliases": [
"jesse-engreitz:220228_8merInsertion-THP1-Amp_PPIF_promoter-BioRep4-FFrep1-BinF-PCRrep1_R2"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2023-12-05T18:45:21.271182+00:00",
"file_format": "fastq",
"file_size": 16353515,
"href": "/sequence-files/IGVFFI6480QWYG/@@download/IGVFFI6480QWYG.fastq.gz",
"md5sum": "bf06287e5cc0a37996fb9a433807e43c",
"s3_uri": "s3://igvf-files/2023/12/05/836cc98e-ce61-47da-a822-184283d434bb/IGVFFI6480QWYG.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-FFRep1-BinF-PCRrep1_S27_R2_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI7479XLVI/",
"accession": "IGVFFI7479XLVI",
"aliases": [
"jesse-engreitz:220228_8merInsertion-THP1-Amp_PPIF_promoter-BioRep4-FFrep1-BinF-PCRrep2_R1"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2023-12-05T18:38:57.908102+00:00",
"file_format": "fastq",
"file_size": 8123978,
"href": "/sequence-files/IGVFFI7479XLVI/@@download/IGVFFI7479XLVI.fastq.gz",
"md5sum": "f0f7bbb77fba5daa20ece42f6b7ff716",
"s3_uri": "s3://igvf-files/2023/12/05/205b5046-dd59-4438-b070-7398d836b966/IGVFFI7479XLVI.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-FFRep1-BinF-PCRrep2_S123_R1_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI9569VGFF/",
"accession": "IGVFFI9569VGFF",
"aliases": [
"jesse-engreitz:220228_8merInsertion-THP1-Amp_PPIF_promoter-BioRep4-FFrep1-BinF-PCRrep2_R2"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2023-12-05T18:51:49.321465+00:00",
"file_format": "fastq",
"file_size": 18108718,
"href": "/sequence-files/IGVFFI9569VGFF/@@download/IGVFFI9569VGFF.fastq.gz",
"md5sum": "dc516ad2a58486b78ce3c4daac32ec42",
"s3_uri": "s3://igvf-files/2023/12/05/e3d93e5c-19e2-4663-8e9e-a591cf9d7056/IGVFFI9569VGFF.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-FFRep1-BinF-PCRrep2_S123_R2_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI6053TTFN/",
"accession": "IGVFFI6053TTFN",
"aliases": [
"jesse-engreitz:220228_8merInsertion-THP1-Amp_PPIF_promoter-BioRep4-FFrep1-BinF-PCRrep2_I2"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2023-12-05T19:16:44.199920+00:00",
"file_format": "fastq",
"file_size": 2813021,
"href": "/sequence-files/IGVFFI6053TTFN/@@download/IGVFFI6053TTFN.fastq.gz",
"md5sum": "ae4f2ecd9198b0a65dd1aef604f7bc35",
"s3_uri": "s3://igvf-files/2023/12/05/354fe251-5785-4e91-894c-1d6ccb0dde80/IGVFFI6053TTFN.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-FFRep1-BinF-PCRrep2_S123_I2_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": "2023-12-20T23:09:24.772202+00:00",
"samples": [
{
"@id": "/in-vitro-systems/IGVFSM4555JSOF/",
"@type": [
"InVitroSystem",
"Biosample",
"Sample",
"Item"
],
"accession": "IGVFSM4555JSOF",
"aliases": [
"jesse-engreitz:220228_8merInsertion-THP1-Amp_PPIF_promoter-BioRep4-FFrep1-BinF"
],
"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 90-100% 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": "2023-12-05T18:32:40.981762+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": "70f4d24b-a8be-4912-8482-a22b37c827c8"
}