{
"@context": "/terms/",
"@id": "/measurement-sets/IGVFDS3851CVMG/",
"@type": [
"MeasurementSet",
"FileSet",
"Item"
],
"accession": "IGVFDS3851CVMG",
"aliases": [
"jesse-engreitz:220228_8merInsertion-THP1-Amp_PPIF_promoter-BioRep4-FFrep2-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 [IGVFSM4767DNSQ](/in-vitro-systems/IGVFSM4767DNSQ/) 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/IGVFSM4767DNSQ/"
},
{
"category": "missing publication",
"detail": "In vitro system [IGVFSM4767DNSQ](/in-vitro-systems/IGVFSM4767DNSQ/) 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/IGVFSM4767DNSQ/"
},
{
"category": "missing publication",
"detail": "Measurement set [IGVFDS3851CVMG](/measurement-sets/IGVFDS3851CVMG/) 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/IGVFDS3851CVMG/"
},
{
"category": "missing sequencing kit",
"detail": "Measurement set [IGVFDS3851CVMG](/measurement-sets/IGVFDS3851CVMG/) has sequence file(s) [IGVFFI0974OECC](/sequence-files/IGVFFI0974OECC/), [IGVFFI1034OOZE](/sequence-files/IGVFFI1034OOZE/), [IGVFFI4673VWKV](/sequence-files/IGVFFI4673VWKV/), [IGVFFI3007IMGH](/sequence-files/IGVFFI3007IMGH/), [IGVFFI7867ZHID](/sequence-files/IGVFFI7867ZHID/), [IGVFFI5395UPMU](/sequence-files/IGVFFI5395UPMU/), [IGVFFI7943UMKL](/sequence-files/IGVFFI7943UMKL/), [IGVFFI3629TKNF](/sequence-files/IGVFFI3629TKNF/) 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/IGVFDS3851CVMG/"
},
{
"category": "missing sequence specification",
"detail": "Measurement set [IGVFDS3851CVMG](/measurement-sets/IGVFDS3851CVMG/) has sequence file(s): [IGVFFI0974OECC](/sequence-files/IGVFFI0974OECC/), [IGVFFI1034OOZE](/sequence-files/IGVFFI1034OOZE/), [IGVFFI4673VWKV](/sequence-files/IGVFFI4673VWKV/), [IGVFFI3007IMGH](/sequence-files/IGVFFI3007IMGH/), [IGVFFI7867ZHID](/sequence-files/IGVFFI7867ZHID/), [IGVFFI5395UPMU](/sequence-files/IGVFFI5395UPMU/), [IGVFFI7943UMKL](/sequence-files/IGVFFI7943UMKL/), [IGVFFI3629TKNF](/sequence-files/IGVFFI3629TKNF/) 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/IGVFDS3851CVMG/"
}
],
"WARNING": [
{
"category": "missing auxiliary set",
"detail": "Measurement set [IGVFDS3851CVMG](/measurement-sets/IGVFDS3851CVMG/) 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/IGVFDS3851CVMG/"
}
]
},
"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": "2023-11-30T22:46:50.960745+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/IGVFFI0974OECC/",
"accession": "IGVFFI0974OECC",
"aliases": [
"jesse-engreitz:220228_8merInsertion-THP1-Amp_PPIF_promoter-BioRep4-FFrep2-BinD-PCRrep1_I1"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2023-12-05T18:58:55.264175+00:00",
"file_format": "fastq",
"file_size": 2928630,
"href": "/sequence-files/IGVFFI0974OECC/@@download/IGVFFI0974OECC.fastq.gz",
"s3_uri": "s3://igvf-files/2023/12/05/f59f5ea5-f1b8-41b9-8364-e84475d69acb/IGVFFI0974OECC.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-BinD-PCRrep1_S32_I1_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI1034OOZE/",
"accession": "IGVFFI1034OOZE",
"aliases": [
"jesse-engreitz:220228_8merInsertion-THP1-Amp_PPIF_promoter-BioRep4-FFrep2-BinD-PCRrep1_R2"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2023-12-05T18:46:06.981034+00:00",
"file_format": "fastq",
"file_size": 16413205,
"href": "/sequence-files/IGVFFI1034OOZE/@@download/IGVFFI1034OOZE.fastq.gz",
"s3_uri": "s3://igvf-files/2023/12/05/5da0909f-c7a1-4abd-96c2-953b19a16efa/IGVFFI1034OOZE.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-BinD-PCRrep1_S32_R2_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI4673VWKV/",
"accession": "IGVFFI4673VWKV",
"aliases": [
"jesse-engreitz:220228_8merInsertion-THP1-Amp_PPIF_promoter-BioRep4-FFrep2-BinD-PCRrep2_I2"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2023-12-05T19:17:27.639078+00:00",
"file_format": "fastq",
"file_size": 2978738,
"href": "/sequence-files/IGVFFI4673VWKV/@@download/IGVFFI4673VWKV.fastq.gz",
"s3_uri": "s3://igvf-files/2023/12/05/314700d8-7d2a-4d31-8ec5-f482018ef1db/IGVFFI4673VWKV.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-BinD-PCRrep2_S128_I2_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI3007IMGH/",
"accession": "IGVFFI3007IMGH",
"aliases": [
"jesse-engreitz:220228_8merInsertion-THP1-Amp_PPIF_promoter-BioRep4-FFrep2-BinD-PCRrep1_I2"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2023-12-05T19:11:20.931777+00:00",
"file_format": "fastq",
"file_size": 2836880,
"href": "/sequence-files/IGVFFI3007IMGH/@@download/IGVFFI3007IMGH.fastq.gz",
"s3_uri": "s3://igvf-files/2023/12/05/544d205c-42e1-427c-99d2-51b8687a09e7/IGVFFI3007IMGH.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-BinD-PCRrep1_S32_I2_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI7867ZHID/",
"accession": "IGVFFI7867ZHID",
"aliases": [
"jesse-engreitz:220228_8merInsertion-THP1-Amp_PPIF_promoter-BioRep4-FFrep2-BinD-PCRrep2_I1"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2023-12-05T19:05:11.849106+00:00",
"file_format": "fastq",
"file_size": 3096302,
"href": "/sequence-files/IGVFFI7867ZHID/@@download/IGVFFI7867ZHID.fastq.gz",
"s3_uri": "s3://igvf-files/2023/12/05/d3557948-c575-40bc-9123-97bb61ed96ea/IGVFFI7867ZHID.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-BinD-PCRrep2_S128_I1_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI5395UPMU/",
"accession": "IGVFFI5395UPMU",
"aliases": [
"jesse-engreitz:220228_8merInsertion-THP1-Amp_PPIF_promoter-BioRep4-FFrep2-BinD-PCRrep2_R1"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2023-12-05T18:39:42.852215+00:00",
"file_format": "fastq",
"file_size": 8656918,
"href": "/sequence-files/IGVFFI5395UPMU/@@download/IGVFFI5395UPMU.fastq.gz",
"s3_uri": "s3://igvf-files/2023/12/05/319dc83e-c778-457d-b772-230058d2b296/IGVFFI5395UPMU.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-BinD-PCRrep2_S128_R1_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI7943UMKL/",
"accession": "IGVFFI7943UMKL",
"aliases": [
"jesse-engreitz:220228_8merInsertion-THP1-Amp_PPIF_promoter-BioRep4-FFrep2-BinD-PCRrep2_R2"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2023-12-05T18:52:38.951011+00:00",
"file_format": "fastq",
"file_size": 17718038,
"href": "/sequence-files/IGVFFI7943UMKL/@@download/IGVFFI7943UMKL.fastq.gz",
"s3_uri": "s3://igvf-files/2023/12/05/9929e979-7eba-43c5-91b1-71a5a78d6271/IGVFFI7943UMKL.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-BinD-PCRrep2_S128_R2_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI3629TKNF/",
"accession": "IGVFFI3629TKNF",
"aliases": [
"jesse-engreitz:220228_8merInsertion-THP1-Amp_PPIF_promoter-BioRep4-FFrep2-BinD-PCRrep1_R1"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2023-12-05T18:33:26.768190+00:00",
"file_format": "fastq",
"file_size": 8469066,
"href": "/sequence-files/IGVFFI3629TKNF/@@download/IGVFFI3629TKNF.fastq.gz",
"s3_uri": "s3://igvf-files/2023/12/05/147ab992-d17f-4010-b7d1-226e1a157bfd/IGVFFI3629TKNF.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-BinD-PCRrep1_S32_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": "2023-12-20T23:11:07.337483+00:00",
"samples": [
{
"@id": "/in-vitro-systems/IGVFSM4767DNSQ/",
"@type": [
"InVitroSystem",
"Biosample",
"Sample",
"Item"
],
"accession": "IGVFSM4767DNSQ",
"aliases": [
"jesse-engreitz:220228_8merInsertion-THP1-Amp_PPIF_promoter-BioRep4-FFrep2-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": "2023-12-05T18:33:26.768190+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": "da1fd031-3c22-4e03-b1a1-b6398f679869"
}