{
"@context": "/terms/",
"@id": "/measurement-sets/IGVFDS9276HGOM/",
"@type": [
"MeasurementSet",
"FileSet",
"Item"
],
"accession": "IGVFDS9276HGOM",
"aliases": [
"jesse-engreitz:220228_8merInsertion-THP1-Amp_PPIF_promoter-BioRep2-FFrep1-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": "mismatched status",
"detail": "Released in vitro system [IGVFSM7667TLNR](/in-vitro-systems/IGVFSM7667TLNR/) 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/IGVFSM7667TLNR/"
},
{
"category": "missing publication",
"detail": "In vitro system [IGVFSM7667TLNR](/in-vitro-systems/IGVFSM7667TLNR/) 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/IGVFSM7667TLNR/"
},
{
"category": "missing publication",
"detail": "Measurement set [IGVFDS9276HGOM](/measurement-sets/IGVFDS9276HGOM/) 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/IGVFDS9276HGOM/"
},
{
"category": "missing sequencing kit",
"detail": "Measurement set [IGVFDS9276HGOM](/measurement-sets/IGVFDS9276HGOM/) has sequence file(s) [IGVFFI6361QXTI](/sequence-files/IGVFFI6361QXTI/), [IGVFFI6276OHCR](/sequence-files/IGVFFI6276OHCR/), [IGVFFI4095POIY](/sequence-files/IGVFFI4095POIY/), [IGVFFI0620HYBP](/sequence-files/IGVFFI0620HYBP/), [IGVFFI6243HNRD](/sequence-files/IGVFFI6243HNRD/), [IGVFFI1842LAAC](/sequence-files/IGVFFI1842LAAC/), [IGVFFI3327DHAS](/sequence-files/IGVFFI3327DHAS/), [IGVFFI9354QAXO](/sequence-files/IGVFFI9354QAXO/) 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/IGVFDS9276HGOM/"
},
{
"category": "missing sequence specification",
"detail": "Measurement set [IGVFDS9276HGOM](/measurement-sets/IGVFDS9276HGOM/) has sequence file(s): [IGVFFI6361QXTI](/sequence-files/IGVFFI6361QXTI/), [IGVFFI6276OHCR](/sequence-files/IGVFFI6276OHCR/), [IGVFFI4095POIY](/sequence-files/IGVFFI4095POIY/), [IGVFFI0620HYBP](/sequence-files/IGVFFI0620HYBP/), [IGVFFI6243HNRD](/sequence-files/IGVFFI6243HNRD/), [IGVFFI1842LAAC](/sequence-files/IGVFFI1842LAAC/), [IGVFFI3327DHAS](/sequence-files/IGVFFI3327DHAS/), [IGVFFI9354QAXO](/sequence-files/IGVFFI9354QAXO/) 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/IGVFDS9276HGOM/"
}
],
"WARNING": [
{
"category": "missing auxiliary set",
"detail": "Measurement set [IGVFDS9276HGOM](/measurement-sets/IGVFDS9276HGOM/) 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/IGVFDS9276HGOM/"
}
]
},
"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": "2023-11-30T22:46:13.122749+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/IGVFFI6361QXTI/",
"accession": "IGVFFI6361QXTI",
"aliases": [
"jesse-engreitz:220228_8merInsertion-THP1-Amp_PPIF_promoter-BioRep2-FFrep1-BinE-PCRrep2_R2"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2023-12-05T18:45:40.995091+00:00",
"file_format": "fastq",
"file_size": 74198380,
"href": "/sequence-files/IGVFFI6361QXTI/@@download/IGVFFI6361QXTI.fastq.gz",
"s3_uri": "s3://igvf-files/2023/12/05/ed0a1f38-4eec-4f08-ae1d-184dc1262bf6/IGVFFI6361QXTI.fastq.gz",
"sequencing_platform": {
"@id": "/platform-terms/EFO_0008566/",
"status": "released",
"term_name": "Illumina NextSeq 550"
},
"status": "released",
"submitted_file_name": "220228pPPIF-FFSample-6-D21-pPPIF-Amp-pPPIF-2-1-2-BinE_R2_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI6276OHCR/",
"accession": "IGVFFI6276OHCR",
"aliases": [
"jesse-engreitz:220228_8merInsertion-THP1-Amp_PPIF_promoter-BioRep2-FFrep1-BinE-PCRrep2_R1"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2023-12-05T18:33:40.494357+00:00",
"file_format": "fastq",
"file_size": 41041285,
"href": "/sequence-files/IGVFFI6276OHCR/@@download/IGVFFI6276OHCR.fastq.gz",
"s3_uri": "s3://igvf-files/2023/12/05/176448ae-856f-4088-89a0-bc0c6ac06db2/IGVFFI6276OHCR.fastq.gz",
"sequencing_platform": {
"@id": "/platform-terms/EFO_0008566/",
"status": "released",
"term_name": "Illumina NextSeq 550"
},
"status": "released",
"submitted_file_name": "220228pPPIF-FFSample-6-D21-pPPIF-Amp-pPPIF-2-1-2-BinE_R1_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI4095POIY/",
"accession": "IGVFFI4095POIY",
"aliases": [
"jesse-engreitz:220228_8merInsertion-THP1-Amp_PPIF_promoter-BioRep2-FFrep1-BinE-PCRrep2_I1"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2023-12-05T18:56:58.154020+00:00",
"file_format": "fastq",
"file_size": 15770999,
"href": "/sequence-files/IGVFFI4095POIY/@@download/IGVFFI4095POIY.fastq.gz",
"s3_uri": "s3://igvf-files/2023/12/05/3f3877ef-6b19-48de-a79c-5c4a84a4812d/IGVFFI4095POIY.fastq.gz",
"sequencing_platform": {
"@id": "/platform-terms/EFO_0008566/",
"status": "released",
"term_name": "Illumina NextSeq 550"
},
"status": "released",
"submitted_file_name": "220228pPPIF-FFSample-6-D21-pPPIF-Amp-pPPIF-2-1-2-BinE_I1_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI0620HYBP/",
"accession": "IGVFFI0620HYBP",
"aliases": [
"jesse-engreitz:220228_8merInsertion-THP1-Amp_PPIF_promoter-BioRep2-FFrep1-BinE-PCRrep1_R2"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2023-12-05T18:39:38.830523+00:00",
"file_format": "fastq",
"file_size": 73584578,
"href": "/sequence-files/IGVFFI0620HYBP/@@download/IGVFFI0620HYBP.fastq.gz",
"s3_uri": "s3://igvf-files/2023/12/05/d3e6f5ec-c0ba-45b9-9add-76db1b4ac456/IGVFFI0620HYBP.fastq.gz",
"sequencing_platform": {
"@id": "/platform-terms/EFO_0008566/",
"status": "released",
"term_name": "Illumina NextSeq 550"
},
"status": "released",
"submitted_file_name": "220228pPPIF-FFSample-6-D21-pPPIF-Amp-pPPIF-2-1-1-BinE_R2_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI6243HNRD/",
"accession": "IGVFFI6243HNRD",
"aliases": [
"jesse-engreitz:220228_8merInsertion-THP1-Amp_PPIF_promoter-BioRep2-FFrep1-BinE-PCRrep2_I2"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2023-12-05T19:08:04.374854+00:00",
"file_format": "fastq",
"file_size": 14156551,
"href": "/sequence-files/IGVFFI6243HNRD/@@download/IGVFFI6243HNRD.fastq.gz",
"s3_uri": "s3://igvf-files/2023/12/05/84e5aea9-1f69-4e8b-97b5-81143097646e/IGVFFI6243HNRD.fastq.gz",
"sequencing_platform": {
"@id": "/platform-terms/EFO_0008566/",
"status": "released",
"term_name": "Illumina NextSeq 550"
},
"status": "released",
"submitted_file_name": "220228pPPIF-FFSample-6-D21-pPPIF-Amp-pPPIF-2-1-2-BinE_I2_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI1842LAAC/",
"accession": "IGVFFI1842LAAC",
"aliases": [
"jesse-engreitz:220228_8merInsertion-THP1-Amp_PPIF_promoter-BioRep2-FFrep1-BinE-PCRrep1_I2"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2023-12-05T19:02:29.906558+00:00",
"file_format": "fastq",
"file_size": 14048393,
"href": "/sequence-files/IGVFFI1842LAAC/@@download/IGVFFI1842LAAC.fastq.gz",
"s3_uri": "s3://igvf-files/2023/12/05/682b353b-a69d-443d-b077-26ac7e695a90/IGVFFI1842LAAC.fastq.gz",
"sequencing_platform": {
"@id": "/platform-terms/EFO_0008566/",
"status": "released",
"term_name": "Illumina NextSeq 550"
},
"status": "released",
"submitted_file_name": "220228pPPIF-FFSample-6-D21-pPPIF-Amp-pPPIF-2-1-1-BinE_I2_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI3327DHAS/",
"accession": "IGVFFI3327DHAS",
"aliases": [
"jesse-engreitz:220228_8merInsertion-THP1-Amp_PPIF_promoter-BioRep2-FFrep1-BinE-PCRrep1_R1"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2023-12-05T18:27:56.908634+00:00",
"file_format": "fastq",
"file_size": 40952099,
"href": "/sequence-files/IGVFFI3327DHAS/@@download/IGVFFI3327DHAS.fastq.gz",
"s3_uri": "s3://igvf-files/2023/12/05/4d6174b4-c264-465c-8974-afc0c79248b2/IGVFFI3327DHAS.fastq.gz",
"sequencing_platform": {
"@id": "/platform-terms/EFO_0008566/",
"status": "released",
"term_name": "Illumina NextSeq 550"
},
"status": "released",
"submitted_file_name": "220228pPPIF-FFSample-6-D21-pPPIF-Amp-pPPIF-2-1-1-BinE_R1_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI9354QAXO/",
"accession": "IGVFFI9354QAXO",
"aliases": [
"jesse-engreitz:220228_8merInsertion-THP1-Amp_PPIF_promoter-BioRep2-FFrep1-BinE-PCRrep1_I1"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2023-12-05T18:51:15.000570+00:00",
"file_format": "fastq",
"file_size": 15115705,
"href": "/sequence-files/IGVFFI9354QAXO/@@download/IGVFFI9354QAXO.fastq.gz",
"s3_uri": "s3://igvf-files/2023/12/05/2ae5ccc9-617f-4280-a92f-7d0a2e22403b/IGVFFI9354QAXO.fastq.gz",
"sequencing_platform": {
"@id": "/platform-terms/EFO_0008566/",
"status": "released",
"term_name": "Illumina NextSeq 550"
},
"status": "released",
"submitted_file_name": "220228pPPIF-FFSample-6-D21-pPPIF-Amp-pPPIF-2-1-1-BinE_I1_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": "2023-12-20T23:11:14.857466+00:00",
"samples": [
{
"@id": "/in-vitro-systems/IGVFSM7667TLNR/",
"@type": [
"InVitroSystem",
"Biosample",
"Sample",
"Item"
],
"accession": "IGVFSM7667TLNR",
"aliases": [
"jesse-engreitz:220228_8merInsertion-THP1-Amp_PPIF_promoter-BioRep2-FFrep1-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": "2023-12-05T18:27:56.908634+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": "4170b7db-caee-40f1-bbaa-fd1d5b39e873"
}