{
"@context": "/terms/",
"@id": "/measurement-sets/IGVFDS2504PFZO/",
"@type": [
"MeasurementSet",
"FileSet",
"Item"
],
"accession": "IGVFDS2504PFZO",
"aliases": [
"jesse-engreitz:220228_8merInsertion-THP1-Amp_PPIF_promoter-BioRep1-FFrep1-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 [IGVFSM0046YFNI](/in-vitro-systems/IGVFSM0046YFNI/) 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/IGVFSM0046YFNI/"
},
{
"category": "missing publication",
"detail": "In vitro system [IGVFSM0046YFNI](/in-vitro-systems/IGVFSM0046YFNI/) 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/IGVFSM0046YFNI/"
},
{
"category": "missing publication",
"detail": "Measurement set [IGVFDS2504PFZO](/measurement-sets/IGVFDS2504PFZO/) 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/IGVFDS2504PFZO/"
},
{
"category": "missing sequencing kit",
"detail": "Measurement set [IGVFDS2504PFZO](/measurement-sets/IGVFDS2504PFZO/) has sequence file(s) [IGVFFI1428JUKH](/sequence-files/IGVFFI1428JUKH/), [IGVFFI0046WWBL](/sequence-files/IGVFFI0046WWBL/), [IGVFFI6752THKB](/sequence-files/IGVFFI6752THKB/), [IGVFFI7314GTAC](/sequence-files/IGVFFI7314GTAC/), [IGVFFI7043IHYQ](/sequence-files/IGVFFI7043IHYQ/), [IGVFFI5062KEJM](/sequence-files/IGVFFI5062KEJM/), [IGVFFI1729WRWF](/sequence-files/IGVFFI1729WRWF/), [IGVFFI7117NASQ](/sequence-files/IGVFFI7117NASQ/) 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/IGVFDS2504PFZO/"
},
{
"category": "missing sequence specification",
"detail": "Measurement set [IGVFDS2504PFZO](/measurement-sets/IGVFDS2504PFZO/) has sequence file(s): [IGVFFI1428JUKH](/sequence-files/IGVFFI1428JUKH/), [IGVFFI0046WWBL](/sequence-files/IGVFFI0046WWBL/), [IGVFFI6752THKB](/sequence-files/IGVFFI6752THKB/), [IGVFFI7314GTAC](/sequence-files/IGVFFI7314GTAC/), [IGVFFI7043IHYQ](/sequence-files/IGVFFI7043IHYQ/), [IGVFFI5062KEJM](/sequence-files/IGVFFI5062KEJM/), [IGVFFI1729WRWF](/sequence-files/IGVFFI1729WRWF/), [IGVFFI7117NASQ](/sequence-files/IGVFFI7117NASQ/) 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/IGVFDS2504PFZO/"
}
],
"WARNING": [
{
"category": "missing auxiliary set",
"detail": "Measurement set [IGVFDS2504PFZO](/measurement-sets/IGVFDS2504PFZO/) 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/IGVFDS2504PFZO/"
}
]
},
"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": "2023-12-01T00:01:46.655160+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/IGVFFI1428JUKH/",
"accession": "IGVFFI1428JUKH",
"aliases": [
"jesse-engreitz:220228_8merInsertion-THP1-Amp_PPIF_promoter-BioRep1-FFrep1-BinD-PCRrep1_I2"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2023-12-05T18:59:06.419965+00:00",
"file_format": "fastq",
"file_size": 12478602,
"href": "/sequence-files/IGVFFI1428JUKH/@@download/IGVFFI1428JUKH.fastq.gz",
"s3_uri": "s3://igvf-files/2023/12/05/98be089d-86b4-4f38-b83b-128e110fb451/IGVFFI1428JUKH.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-BinD_I2_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI0046WWBL/",
"accession": "IGVFFI0046WWBL",
"aliases": [
"jesse-engreitz:220228_8merInsertion-THP1-Amp_PPIF_promoter-BioRep1-FFrep1-BinD-PCRrep1_R1"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2023-12-05T18:24:27.768762+00:00",
"file_format": "fastq",
"file_size": 36426179,
"href": "/sequence-files/IGVFFI0046WWBL/@@download/IGVFFI0046WWBL.fastq.gz",
"s3_uri": "s3://igvf-files/2023/12/05/98acea11-cec8-454e-aadb-917f76894bf3/IGVFFI0046WWBL.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-BinD_R1_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI6752THKB/",
"accession": "IGVFFI6752THKB",
"aliases": [
"jesse-engreitz:220228_8merInsertion-THP1-Amp_PPIF_promoter-BioRep1-FFrep1-BinD-PCRrep1_I1"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2023-12-05T18:47:53.787752+00:00",
"file_format": "fastq",
"file_size": 13537961,
"href": "/sequence-files/IGVFFI6752THKB/@@download/IGVFFI6752THKB.fastq.gz",
"s3_uri": "s3://igvf-files/2023/12/05/fdf9264f-06c5-4baf-971d-719b9afb0476/IGVFFI6752THKB.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-BinD_I1_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI7314GTAC/",
"accession": "IGVFFI7314GTAC",
"aliases": [
"jesse-engreitz:220228_8merInsertion-THP1-Amp_PPIF_promoter-BioRep1-FFrep1-BinD-PCRrep2_I1"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2023-12-05T18:53:26.878542+00:00",
"file_format": "fastq",
"file_size": 15031585,
"href": "/sequence-files/IGVFFI7314GTAC/@@download/IGVFFI7314GTAC.fastq.gz",
"s3_uri": "s3://igvf-files/2023/12/05/298ce967-67eb-458a-a9c1-92bb5c147c57/IGVFFI7314GTAC.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-BinD_I1_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI7043IHYQ/",
"accession": "IGVFFI7043IHYQ",
"aliases": [
"jesse-engreitz:220228_8merInsertion-THP1-Amp_PPIF_promoter-BioRep1-FFrep1-BinD-PCRrep2_R2"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2023-12-05T18:41:58.318266+00:00",
"file_format": "fastq",
"file_size": 75716125,
"href": "/sequence-files/IGVFFI7043IHYQ/@@download/IGVFFI7043IHYQ.fastq.gz",
"s3_uri": "s3://igvf-files/2023/12/05/a8993d8d-3d73-4ad5-b72f-0dfb5fdba49a/IGVFFI7043IHYQ.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-BinD_R2_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI5062KEJM/",
"accession": "IGVFFI5062KEJM",
"aliases": [
"jesse-engreitz:220228_8merInsertion-THP1-Amp_PPIF_promoter-BioRep1-FFrep1-BinD-PCRrep1_R2"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2023-12-05T18:35:52.486973+00:00",
"file_format": "fastq",
"file_size": 65659412,
"href": "/sequence-files/IGVFFI5062KEJM/@@download/IGVFFI5062KEJM.fastq.gz",
"s3_uri": "s3://igvf-files/2023/12/05/83b8a9f9-e279-4295-a877-564ff17ba0da/IGVFFI5062KEJM.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-BinD_R2_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI1729WRWF/",
"accession": "IGVFFI1729WRWF",
"aliases": [
"jesse-engreitz:220228_8merInsertion-THP1-Amp_PPIF_promoter-BioRep1-FFrep1-BinD-PCRrep2_R1"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2023-12-05T18:30:11.355681+00:00",
"file_format": "fastq",
"file_size": 41692106,
"href": "/sequence-files/IGVFFI1729WRWF/@@download/IGVFFI1729WRWF.fastq.gz",
"s3_uri": "s3://igvf-files/2023/12/05/2c8bd867-c051-4b8a-ac41-a1d6bf06a032/IGVFFI1729WRWF.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-BinD_R1_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI7117NASQ/",
"accession": "IGVFFI7117NASQ",
"aliases": [
"jesse-engreitz:220228_8merInsertion-THP1-Amp_PPIF_promoter-BioRep1-FFrep1-BinD-PCRrep2_I2"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2023-12-05T19:04:38.608975+00:00",
"file_format": "fastq",
"file_size": 14262944,
"href": "/sequence-files/IGVFFI7117NASQ/@@download/IGVFFI7117NASQ.fastq.gz",
"s3_uri": "s3://igvf-files/2023/12/05/a15b3b7a-2784-467b-83a7-420d46691081/IGVFFI7117NASQ.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-BinD_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": "2023-12-20T23:10:00.627205+00:00",
"samples": [
{
"@id": "/in-vitro-systems/IGVFSM0046YFNI/",
"@type": [
"InVitroSystem",
"Biosample",
"Sample",
"Item"
],
"accession": "IGVFSM0046YFNI",
"aliases": [
"jesse-engreitz:220228_8merInsertion-THP1-Amp_PPIF_promoter-BioRep1-FFrep1-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": "2023-12-05T18:24:27.768762+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": "917a9aef-d602-4d1e-b7bb-76ee730cac92"
}