{
"@context": "/terms/",
"@id": "/measurement-sets/IGVFDS0300ELGK/",
"@type": [
"MeasurementSet",
"FileSet",
"Item"
],
"accession": "IGVFDS0300ELGK",
"aliases": [
"jesse-engreitz:220228_8merInsertion-THP1-Amp_PPIF_promoter-BioRep4-FFrep2-BinA_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 [IGVFDS0300ELGK](/measurement-sets/IGVFDS0300ELGK/) 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/IGVFDS0300ELGK/"
},
{
"category": "missing sequencing kit",
"detail": "Measurement set [IGVFDS0300ELGK](/measurement-sets/IGVFDS0300ELGK/) has sequence file(s) [IGVFFI5834MHAJ](/sequence-files/IGVFFI5834MHAJ/), [IGVFFI6027ICQU](/sequence-files/IGVFFI6027ICQU/), [IGVFFI9165WZFZ](/sequence-files/IGVFFI9165WZFZ/), [IGVFFI5146VEEV](/sequence-files/IGVFFI5146VEEV/), [IGVFFI6878SKPS](/sequence-files/IGVFFI6878SKPS/), [IGVFFI0260GPKI](/sequence-files/IGVFFI0260GPKI/), [IGVFFI3876HFLM](/sequence-files/IGVFFI3876HFLM/), [IGVFFI1604QQEC](/sequence-files/IGVFFI1604QQEC/) 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/IGVFDS0300ELGK/"
},
{
"category": "missing sequence specification",
"detail": "Measurement set [IGVFDS0300ELGK](/measurement-sets/IGVFDS0300ELGK/) has sequence file(s): [IGVFFI5834MHAJ](/sequence-files/IGVFFI5834MHAJ/), [IGVFFI6027ICQU](/sequence-files/IGVFFI6027ICQU/), [IGVFFI9165WZFZ](/sequence-files/IGVFFI9165WZFZ/), [IGVFFI5146VEEV](/sequence-files/IGVFFI5146VEEV/), [IGVFFI6878SKPS](/sequence-files/IGVFFI6878SKPS/), [IGVFFI0260GPKI](/sequence-files/IGVFFI0260GPKI/), [IGVFFI3876HFLM](/sequence-files/IGVFFI3876HFLM/), [IGVFFI1604QQEC](/sequence-files/IGVFFI1604QQEC/) 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/IGVFDS0300ELGK/"
},
{
"category": "mismatched status",
"detail": "Released in vitro system [IGVFSM1606JQTG](/in-vitro-systems/IGVFSM1606JQTG/) 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/IGVFSM1606JQTG/"
},
{
"category": "missing publication",
"detail": "In vitro system [IGVFSM1606JQTG](/in-vitro-systems/IGVFSM1606JQTG/) 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/IGVFSM1606JQTG/"
}
],
"WARNING": [
{
"category": "missing auxiliary set",
"detail": "Measurement set [IGVFDS0300ELGK](/measurement-sets/IGVFDS0300ELGK/) 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/IGVFDS0300ELGK/"
}
]
},
"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": "2023-11-30T22:46:47.618585+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/IGVFFI5834MHAJ/",
"accession": "IGVFFI5834MHAJ",
"aliases": [
"jesse-engreitz:220228_8merInsertion-THP1-Amp_PPIF_promoter-BioRep4-FFrep2-BinA-PCRrep2_I1"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2023-12-05T19:04:45.772788+00:00",
"file_format": "fastq",
"file_size": 2724187,
"href": "/sequence-files/IGVFFI5834MHAJ/@@download/IGVFFI5834MHAJ.fastq.gz",
"s3_uri": "s3://igvf-files/2023/12/05/5c530782-312c-4696-bfa3-3fadd7e7c513/IGVFFI5834MHAJ.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-BinA-PCRrep2_S125_I1_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI6027ICQU/",
"accession": "IGVFFI6027ICQU",
"aliases": [
"jesse-engreitz:220228_8merInsertion-THP1-Amp_PPIF_promoter-BioRep4-FFrep2-BinA-PCRrep1_I1"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2023-12-05T18:58:29.214160+00:00",
"file_format": "fastq",
"file_size": 2637150,
"href": "/sequence-files/IGVFFI6027ICQU/@@download/IGVFFI6027ICQU.fastq.gz",
"s3_uri": "s3://igvf-files/2023/12/05/c956d52b-ed86-4354-aa7c-dab92314a14e/IGVFFI6027ICQU.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-BinA-PCRrep1_S29_I1_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI9165WZFZ/",
"accession": "IGVFFI9165WZFZ",
"aliases": [
"jesse-engreitz:220228_8merInsertion-THP1-Amp_PPIF_promoter-BioRep4-FFrep2-BinA-PCRrep1_R1"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2023-12-05T18:32:59.987441+00:00",
"file_format": "fastq",
"file_size": 7720285,
"href": "/sequence-files/IGVFFI9165WZFZ/@@download/IGVFFI9165WZFZ.fastq.gz",
"s3_uri": "s3://igvf-files/2023/12/05/c9a5f69a-2116-4d7c-9360-5bbc00084d93/IGVFFI9165WZFZ.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-BinA-PCRrep1_S29_R1_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI5146VEEV/",
"accession": "IGVFFI5146VEEV",
"aliases": [
"jesse-engreitz:220228_8merInsertion-THP1-Amp_PPIF_promoter-BioRep4-FFrep2-BinA-PCRrep1_I2"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2023-12-05T19:10:55.530916+00:00",
"file_format": "fastq",
"file_size": 2500524,
"href": "/sequence-files/IGVFFI5146VEEV/@@download/IGVFFI5146VEEV.fastq.gz",
"s3_uri": "s3://igvf-files/2023/12/05/cbc3d9d1-ae9c-4280-b192-2a95c9d9f62f/IGVFFI5146VEEV.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-BinA-PCRrep1_S29_I2_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI6878SKPS/",
"accession": "IGVFFI6878SKPS",
"aliases": [
"jesse-engreitz:220228_8merInsertion-THP1-Amp_PPIF_promoter-BioRep4-FFrep2-BinA-PCRrep2_R1"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2023-12-05T18:39:15.904310+00:00",
"file_format": "fastq",
"file_size": 7858283,
"href": "/sequence-files/IGVFFI6878SKPS/@@download/IGVFFI6878SKPS.fastq.gz",
"s3_uri": "s3://igvf-files/2023/12/05/bf63a79f-a42b-4665-923d-87f4436f8781/IGVFFI6878SKPS.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-BinA-PCRrep2_S125_R1_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI0260GPKI/",
"accession": "IGVFFI0260GPKI",
"aliases": [
"jesse-engreitz:220228_8merInsertion-THP1-Amp_PPIF_promoter-BioRep4-FFrep2-BinA-PCRrep2_I2"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2023-12-05T19:17:01.574366+00:00",
"file_format": "fastq",
"file_size": 2597004,
"href": "/sequence-files/IGVFFI0260GPKI/@@download/IGVFFI0260GPKI.fastq.gz",
"s3_uri": "s3://igvf-files/2023/12/05/07fd502a-547f-4302-8c52-e04e09b177ef/IGVFFI0260GPKI.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-BinA-PCRrep2_S125_I2_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI3876HFLM/",
"accession": "IGVFFI3876HFLM",
"aliases": [
"jesse-engreitz:220228_8merInsertion-THP1-Amp_PPIF_promoter-BioRep4-FFrep2-BinA-PCRrep1_R2"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2023-12-05T18:45:39.613343+00:00",
"file_format": "fastq",
"file_size": 14900744,
"href": "/sequence-files/IGVFFI3876HFLM/@@download/IGVFFI3876HFLM.fastq.gz",
"s3_uri": "s3://igvf-files/2023/12/05/9889af53-bab5-4930-a960-143f1a65aaad/IGVFFI3876HFLM.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-BinA-PCRrep1_S29_R2_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI1604QQEC/",
"accession": "IGVFFI1604QQEC",
"aliases": [
"jesse-engreitz:220228_8merInsertion-THP1-Amp_PPIF_promoter-BioRep4-FFrep2-BinA-PCRrep2_R2"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2023-12-05T18:52:07.735351+00:00",
"file_format": "fastq",
"file_size": 15778798,
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"s3_uri": "s3://igvf-files/2023/12/05/53a82f37-2da4-4c4e-8dcd-9c7d800c8e73/IGVFFI1604QQEC.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-BinA-PCRrep2_S125_R2_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": "2023-12-20T23:09:48.095219+00:00",
"samples": [
{
"@id": "/in-vitro-systems/IGVFSM1606JQTG/",
"@type": [
"InVitroSystem",
"Biosample",
"Sample",
"Item"
],
"accession": "IGVFSM1606JQTG",
"aliases": [
"jesse-engreitz:220228_8merInsertion-THP1-Amp_PPIF_promoter-BioRep4-FFrep2-BinA"
],
"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 0-10% 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": "2023-12-05T18:32:59.987441+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": "288b7aa2-e5b6-4840-a3e4-40add841df02"
}