{
"@context": "/terms/",
"@id": "/measurement-sets/IGVFDS8067PUZX/",
"@type": [
"MeasurementSet",
"FileSet",
"Item"
],
"accession": "IGVFDS8067PUZX",
"aliases": [
"jesse-engreitz:220228_8merInsertion-THP1-Amp_PPIF_promoter-BioRep4-FFrep2-BinC_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 [IGVFDS8067PUZX](/measurement-sets/IGVFDS8067PUZX/) 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/IGVFDS8067PUZX/"
},
{
"category": "missing sequencing kit",
"detail": "Measurement set [IGVFDS8067PUZX](/measurement-sets/IGVFDS8067PUZX/) has sequence file(s) [IGVFFI6879FDSU](/sequence-files/IGVFFI6879FDSU/), [IGVFFI7637LIGF](/sequence-files/IGVFFI7637LIGF/), [IGVFFI3829ODVU](/sequence-files/IGVFFI3829ODVU/), [IGVFFI9360VWEF](/sequence-files/IGVFFI9360VWEF/), [IGVFFI3413VNUA](/sequence-files/IGVFFI3413VNUA/), [IGVFFI8859VHIB](/sequence-files/IGVFFI8859VHIB/), [IGVFFI8305XHRM](/sequence-files/IGVFFI8305XHRM/), [IGVFFI8961NDMV](/sequence-files/IGVFFI8961NDMV/) 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/IGVFDS8067PUZX/"
},
{
"category": "missing sequence specification",
"detail": "Measurement set [IGVFDS8067PUZX](/measurement-sets/IGVFDS8067PUZX/) has sequence file(s): [IGVFFI6879FDSU](/sequence-files/IGVFFI6879FDSU/), [IGVFFI7637LIGF](/sequence-files/IGVFFI7637LIGF/), [IGVFFI3829ODVU](/sequence-files/IGVFFI3829ODVU/), [IGVFFI9360VWEF](/sequence-files/IGVFFI9360VWEF/), [IGVFFI3413VNUA](/sequence-files/IGVFFI3413VNUA/), [IGVFFI8859VHIB](/sequence-files/IGVFFI8859VHIB/), [IGVFFI8305XHRM](/sequence-files/IGVFFI8305XHRM/), [IGVFFI8961NDMV](/sequence-files/IGVFFI8961NDMV/) 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/IGVFDS8067PUZX/"
},
{
"category": "mismatched status",
"detail": "Released in vitro system [IGVFSM0701VWIZ](/in-vitro-systems/IGVFSM0701VWIZ/) 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/IGVFSM0701VWIZ/"
},
{
"category": "missing publication",
"detail": "In vitro system [IGVFSM0701VWIZ](/in-vitro-systems/IGVFSM0701VWIZ/) 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/IGVFSM0701VWIZ/"
}
],
"WARNING": [
{
"category": "missing auxiliary set",
"detail": "Measurement set [IGVFDS8067PUZX](/measurement-sets/IGVFDS8067PUZX/) 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/IGVFDS8067PUZX/"
}
]
},
"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": "2023-11-30T22:46:50.164515+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/IGVFFI6879FDSU/",
"accession": "IGVFFI6879FDSU",
"aliases": [
"jesse-engreitz:220228_8merInsertion-THP1-Amp_PPIF_promoter-BioRep4-FFrep2-BinC-PCRrep1_R1"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2023-12-05T18:33:17.696323+00:00",
"file_format": "fastq",
"file_size": 8635018,
"href": "/sequence-files/IGVFFI6879FDSU/@@download/IGVFFI6879FDSU.fastq.gz",
"s3_uri": "s3://igvf-files/2023/12/05/fbf10c29-bb9a-4945-9958-2bb80c04215d/IGVFFI6879FDSU.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-BinC-PCRrep1_S31_R1_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI7637LIGF/",
"accession": "IGVFFI7637LIGF",
"aliases": [
"jesse-engreitz:220228_8merInsertion-THP1-Amp_PPIF_promoter-BioRep4-FFrep2-BinC-PCRrep2_I2"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2023-12-05T19:17:19.012359+00:00",
"file_format": "fastq",
"file_size": 2996954,
"href": "/sequence-files/IGVFFI7637LIGF/@@download/IGVFFI7637LIGF.fastq.gz",
"s3_uri": "s3://igvf-files/2023/12/05/0371b3e4-dc1b-4229-989e-7eb885ab525a/IGVFFI7637LIGF.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-BinC-PCRrep2_S127_I2_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI3829ODVU/",
"accession": "IGVFFI3829ODVU",
"aliases": [
"jesse-engreitz:220228_8merInsertion-THP1-Amp_PPIF_promoter-BioRep4-FFrep2-BinC-PCRrep2_R2"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2023-12-05T18:52:25.787749+00:00",
"file_format": "fastq",
"file_size": 17589164,
"href": "/sequence-files/IGVFFI3829ODVU/@@download/IGVFFI3829ODVU.fastq.gz",
"s3_uri": "s3://igvf-files/2023/12/05/2bcd9cda-3f1f-45ab-9552-bb1d2aa302ee/IGVFFI3829ODVU.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-BinC-PCRrep2_S127_R2_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI9360VWEF/",
"accession": "IGVFFI9360VWEF",
"aliases": [
"jesse-engreitz:220228_8merInsertion-THP1-Amp_PPIF_promoter-BioRep4-FFrep2-BinC-PCRrep1_I2"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2023-12-05T19:11:12.270711+00:00",
"file_format": "fastq",
"file_size": 2856894,
"href": "/sequence-files/IGVFFI9360VWEF/@@download/IGVFFI9360VWEF.fastq.gz",
"s3_uri": "s3://igvf-files/2023/12/05/87d81f30-fcc2-4f85-bab2-674258855132/IGVFFI9360VWEF.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-BinC-PCRrep1_S31_I2_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI3413VNUA/",
"accession": "IGVFFI3413VNUA",
"aliases": [
"jesse-engreitz:220228_8merInsertion-THP1-Amp_PPIF_promoter-BioRep4-FFrep2-BinC-PCRrep1_R2"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2023-12-05T18:45:57.906806+00:00",
"file_format": "fastq",
"file_size": 16593442,
"href": "/sequence-files/IGVFFI3413VNUA/@@download/IGVFFI3413VNUA.fastq.gz",
"s3_uri": "s3://igvf-files/2023/12/05/682229de-364c-462a-843b-f8e5ec367ac9/IGVFFI3413VNUA.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-BinC-PCRrep1_S31_R2_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI8859VHIB/",
"accession": "IGVFFI8859VHIB",
"aliases": [
"jesse-engreitz:220228_8merInsertion-THP1-Amp_PPIF_promoter-BioRep4-FFrep2-BinC-PCRrep2_R1"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2023-12-05T18:39:33.756214+00:00",
"file_format": "fastq",
"file_size": 8851507,
"href": "/sequence-files/IGVFFI8859VHIB/@@download/IGVFFI8859VHIB.fastq.gz",
"s3_uri": "s3://igvf-files/2023/12/05/fb913ad4-45c8-4437-bf9a-8fc92e876912/IGVFFI8859VHIB.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-BinC-PCRrep2_S127_R1_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI8305XHRM/",
"accession": "IGVFFI8305XHRM",
"aliases": [
"jesse-engreitz:220228_8merInsertion-THP1-Amp_PPIF_promoter-BioRep4-FFrep2-BinC-PCRrep1_I1"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2023-12-05T18:58:46.579860+00:00",
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"file_size": 2993764,
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"s3_uri": "s3://igvf-files/2023/12/05/6578508f-2e27-4623-8b88-f876f0ed05e5/IGVFFI8305XHRM.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-BinC-PCRrep1_S31_I1_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI8961NDMV/",
"accession": "IGVFFI8961NDMV",
"aliases": [
"jesse-engreitz:220228_8merInsertion-THP1-Amp_PPIF_promoter-BioRep4-FFrep2-BinC-PCRrep2_I1"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2023-12-05T19:05:03.120534+00:00",
"file_format": "fastq",
"file_size": 3107954,
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"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-BinC-PCRrep2_S127_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": "2023-12-20T23:10:10.560700+00:00",
"samples": [
{
"@id": "/in-vitro-systems/IGVFSM0701VWIZ/",
"@type": [
"InVitroSystem",
"Biosample",
"Sample",
"Item"
],
"accession": "IGVFSM0701VWIZ",
"aliases": [
"jesse-engreitz:220228_8merInsertion-THP1-Amp_PPIF_promoter-BioRep4-FFrep2-BinC"
],
"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 35-45% 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": "2023-12-05T18:33:17.696323+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": "b79adb23-fd2f-4d39-a076-607346d850e4"
}