{
"@context": "/terms/",
"@id": "/measurement-sets/IGVFDS9444IQCJ/",
"@type": [
"MeasurementSet",
"FileSet",
"Item"
],
"accession": "IGVFDS9444IQCJ",
"aliases": [
"jesse-engreitz:220228_8merInsertion-THP1-Amp_PPIF_promoter-BioRep3-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": "mismatched status",
"detail": "Released in vitro system [IGVFSM3490JPYE](/in-vitro-systems/IGVFSM3490JPYE/) 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/IGVFSM3490JPYE/"
},
{
"category": "missing publication",
"detail": "In vitro system [IGVFSM3490JPYE](/in-vitro-systems/IGVFSM3490JPYE/) 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/IGVFSM3490JPYE/"
},
{
"category": "missing publication",
"detail": "Measurement set [IGVFDS9444IQCJ](/measurement-sets/IGVFDS9444IQCJ/) 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/IGVFDS9444IQCJ/"
},
{
"category": "missing sequencing kit",
"detail": "Measurement set [IGVFDS9444IQCJ](/measurement-sets/IGVFDS9444IQCJ/) has sequence file(s) [IGVFFI0898YNWS](/sequence-files/IGVFFI0898YNWS/), [IGVFFI7789DVWP](/sequence-files/IGVFFI7789DVWP/), [IGVFFI4319ZVUO](/sequence-files/IGVFFI4319ZVUO/), [IGVFFI1846BTVL](/sequence-files/IGVFFI1846BTVL/), [IGVFFI5595WMRY](/sequence-files/IGVFFI5595WMRY/), [IGVFFI9043LOIU](/sequence-files/IGVFFI9043LOIU/), [IGVFFI8035IDKN](/sequence-files/IGVFFI8035IDKN/), [IGVFFI4923YKLM](/sequence-files/IGVFFI4923YKLM/) 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/IGVFDS9444IQCJ/"
},
{
"category": "missing sequence specification",
"detail": "Measurement set [IGVFDS9444IQCJ](/measurement-sets/IGVFDS9444IQCJ/) has sequence file(s): [IGVFFI0898YNWS](/sequence-files/IGVFFI0898YNWS/), [IGVFFI7789DVWP](/sequence-files/IGVFFI7789DVWP/), [IGVFFI4319ZVUO](/sequence-files/IGVFFI4319ZVUO/), [IGVFFI1846BTVL](/sequence-files/IGVFFI1846BTVL/), [IGVFFI5595WMRY](/sequence-files/IGVFFI5595WMRY/), [IGVFFI9043LOIU](/sequence-files/IGVFFI9043LOIU/), [IGVFFI8035IDKN](/sequence-files/IGVFFI8035IDKN/), [IGVFFI4923YKLM](/sequence-files/IGVFFI4923YKLM/) 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/IGVFDS9444IQCJ/"
}
],
"WARNING": [
{
"category": "missing auxiliary set",
"detail": "Measurement set [IGVFDS9444IQCJ](/measurement-sets/IGVFDS9444IQCJ/) 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/IGVFDS9444IQCJ/"
}
]
},
"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": "2023-11-30T22:46:29.618675+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/IGVFFI0898YNWS/",
"accession": "IGVFFI0898YNWS",
"aliases": [
"jesse-engreitz:220228_8merInsertion-THP1-Amp_PPIF_promoter-BioRep3-FFrep2-BinA-PCRrep1_R1"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2023-12-05T18:29:47.934076+00:00",
"file_format": "fastq",
"file_size": 8609389,
"href": "/sequence-files/IGVFFI0898YNWS/@@download/IGVFFI0898YNWS.fastq.gz",
"s3_uri": "s3://igvf-files/2023/12/05/182e794f-01b0-463a-8d78-c4e95498687c/IGVFFI0898YNWS.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-BioRep1-FFRep2-BinA-PCRrep1_S8_R1_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI7789DVWP/",
"accession": "IGVFFI7789DVWP",
"aliases": [
"jesse-engreitz:220228_8merInsertion-THP1-Amp_PPIF_promoter-BioRep3-FFrep2-BinA-PCRrep2_R1"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2023-12-05T18:36:07.107148+00:00",
"file_format": "fastq",
"file_size": 8783731,
"href": "/sequence-files/IGVFFI7789DVWP/@@download/IGVFFI7789DVWP.fastq.gz",
"s3_uri": "s3://igvf-files/2023/12/05/9f678b18-a03b-4535-907f-eba64ebc8f1b/IGVFFI7789DVWP.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-BioRep1-FFRep2-BinA-PCRrep2_S104_R1_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI4319ZVUO/",
"accession": "IGVFFI4319ZVUO",
"aliases": [
"jesse-engreitz:220228_8merInsertion-THP1-Amp_PPIF_promoter-BioRep3-FFrep2-BinA-PCRrep1_I1"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2023-12-05T18:55:20.459088+00:00",
"file_format": "fastq",
"file_size": 3002650,
"href": "/sequence-files/IGVFFI4319ZVUO/@@download/IGVFFI4319ZVUO.fastq.gz",
"s3_uri": "s3://igvf-files/2023/12/05/0188e75a-bc40-42d2-8681-c6efeb599700/IGVFFI4319ZVUO.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-BioRep1-FFRep2-BinA-PCRrep1_S8_I1_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI1846BTVL/",
"accession": "IGVFFI1846BTVL",
"aliases": [
"jesse-engreitz:220228_8merInsertion-THP1-Amp_PPIF_promoter-BioRep3-FFrep2-BinA-PCRrep2_R2"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2023-12-05T18:48:51.739951+00:00",
"file_format": "fastq",
"file_size": 17298891,
"href": "/sequence-files/IGVFFI1846BTVL/@@download/IGVFFI1846BTVL.fastq.gz",
"s3_uri": "s3://igvf-files/2023/12/05/8e5caee4-fc26-4674-a153-2711a9bb1ea2/IGVFFI1846BTVL.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-BioRep1-FFRep2-BinA-PCRrep2_S104_R2_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI5595WMRY/",
"accession": "IGVFFI5595WMRY",
"aliases": [
"jesse-engreitz:220228_8merInsertion-THP1-Amp_PPIF_promoter-BioRep3-FFrep2-BinA-PCRrep1_R2"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2023-12-05T18:42:27.334283+00:00",
"file_format": "fastq",
"file_size": 16489650,
"href": "/sequence-files/IGVFFI5595WMRY/@@download/IGVFFI5595WMRY.fastq.gz",
"s3_uri": "s3://igvf-files/2023/12/05/70a0dd4f-53dc-4c0d-9710-855c99c30d55/IGVFFI5595WMRY.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-BioRep1-FFRep2-BinA-PCRrep1_S8_R2_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI9043LOIU/",
"accession": "IGVFFI9043LOIU",
"aliases": [
"jesse-engreitz:220228_8merInsertion-THP1-Amp_PPIF_promoter-BioRep3-FFrep2-BinA-PCRrep2_I1"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2023-12-05T19:01:40.104921+00:00",
"file_format": "fastq",
"file_size": 3065691,
"href": "/sequence-files/IGVFFI9043LOIU/@@download/IGVFFI9043LOIU.fastq.gz",
"s3_uri": "s3://igvf-files/2023/12/05/ac200bda-d097-418d-88d2-400f4a1902be/IGVFFI9043LOIU.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-BioRep1-FFRep2-BinA-PCRrep2_S104_I1_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI8035IDKN/",
"accession": "IGVFFI8035IDKN",
"aliases": [
"jesse-engreitz:220228_8merInsertion-THP1-Amp_PPIF_promoter-BioRep3-FFrep2-BinA-PCRrep1_I2"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2023-12-05T19:07:47.634118+00:00",
"file_format": "fastq",
"file_size": 2781690,
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"s3_uri": "s3://igvf-files/2023/12/05/53f9b5a7-5b79-4c10-979e-0d07e6189f1d/IGVFFI8035IDKN.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-BioRep1-FFRep2-BinA-PCRrep1_S8_I2_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI4923YKLM/",
"accession": "IGVFFI4923YKLM",
"aliases": [
"jesse-engreitz:220228_8merInsertion-THP1-Amp_PPIF_promoter-BioRep3-FFrep2-BinA-PCRrep2_I2"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2023-12-05T19:13:57.611639+00:00",
"file_format": "fastq",
"file_size": 2865278,
"href": "/sequence-files/IGVFFI4923YKLM/@@download/IGVFFI4923YKLM.fastq.gz",
"s3_uri": "s3://igvf-files/2023/12/05/0f6be98f-d9e5-4ae1-a22e-de95a65ce4fb/IGVFFI4923YKLM.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-BioRep1-FFRep2-BinA-PCRrep2_S104_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": "2023-12-20T23:09:46.871239+00:00",
"samples": [
{
"@id": "/in-vitro-systems/IGVFSM3490JPYE/",
"@type": [
"InVitroSystem",
"Biosample",
"Sample",
"Item"
],
"accession": "IGVFSM3490JPYE",
"aliases": [
"jesse-engreitz:220228_8merInsertion-THP1-Amp_PPIF_promoter-BioRep3-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": "2023-12-05T18:29:47.934076+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": "9903f5b4-566f-4750-ba30-54ca2e2f65ba"
}