{
"@context": "/terms/",
"@id": "/measurement-sets/IGVFDS6756WKPU/",
"@type": [
"MeasurementSet",
"FileSet",
"Item"
],
"accession": "IGVFDS6756WKPU",
"aliases": [
"jesse-engreitz:220228_8merInsertion-THP1-Amp_PPIF_promoter-BioRep4-FFrep1-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 [IGVFSM7338BXZP](/in-vitro-systems/IGVFSM7338BXZP/) 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/IGVFSM7338BXZP/"
},
{
"category": "missing publication",
"detail": "In vitro system [IGVFSM7338BXZP](/in-vitro-systems/IGVFSM7338BXZP/) 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/IGVFSM7338BXZP/"
},
{
"category": "missing publication",
"detail": "Measurement set [IGVFDS6756WKPU](/measurement-sets/IGVFDS6756WKPU/) 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/IGVFDS6756WKPU/"
},
{
"category": "missing sequencing kit",
"detail": "Measurement set [IGVFDS6756WKPU](/measurement-sets/IGVFDS6756WKPU/) has sequence file(s) [IGVFFI2983PWXS](/sequence-files/IGVFFI2983PWXS/), [IGVFFI1754XQJY](/sequence-files/IGVFFI1754XQJY/), [IGVFFI6561JCKT](/sequence-files/IGVFFI6561JCKT/), [IGVFFI7214MLEI](/sequence-files/IGVFFI7214MLEI/), [IGVFFI0797YDWG](/sequence-files/IGVFFI0797YDWG/), [IGVFFI3543WVWH](/sequence-files/IGVFFI3543WVWH/), [IGVFFI3594OXIX](/sequence-files/IGVFFI3594OXIX/), [IGVFFI6830NYRY](/sequence-files/IGVFFI6830NYRY/) 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/IGVFDS6756WKPU/"
},
{
"category": "missing sequence specification",
"detail": "Measurement set [IGVFDS6756WKPU](/measurement-sets/IGVFDS6756WKPU/) has sequence file(s): [IGVFFI2983PWXS](/sequence-files/IGVFFI2983PWXS/), [IGVFFI1754XQJY](/sequence-files/IGVFFI1754XQJY/), [IGVFFI6561JCKT](/sequence-files/IGVFFI6561JCKT/), [IGVFFI7214MLEI](/sequence-files/IGVFFI7214MLEI/), [IGVFFI0797YDWG](/sequence-files/IGVFFI0797YDWG/), [IGVFFI3543WVWH](/sequence-files/IGVFFI3543WVWH/), [IGVFFI3594OXIX](/sequence-files/IGVFFI3594OXIX/), [IGVFFI6830NYRY](/sequence-files/IGVFFI6830NYRY/) 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/IGVFDS6756WKPU/"
}
],
"WARNING": [
{
"category": "missing auxiliary set",
"detail": "Measurement set [IGVFDS6756WKPU](/measurement-sets/IGVFDS6756WKPU/) 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/IGVFDS6756WKPU/"
}
]
},
"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": "2023-11-30T22:46:41.860175+00:00",
"data_use_limitation_summaries": [
"no certificate"
],
"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/IGVFFI2983PWXS/",
"accession": "IGVFFI2983PWXS",
"aliases": [
"jesse-engreitz:220228_8merInsertion-THP1-Amp_PPIF_promoter-BioRep4-FFrep1-BinA-PCRrep1_R2"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2023-12-05T18:44:35.485744+00:00",
"file_format": "fastq",
"file_size": 15916056,
"href": "/sequence-files/IGVFFI2983PWXS/@@download/IGVFFI2983PWXS.fastq.gz",
"md5sum": "3077144d21d28ab3d6861df8b5b36832",
"s3_uri": "s3://igvf-files/2023/12/05/dc44a5ec-93b2-4547-8f25-778fce7f564e/IGVFFI2983PWXS.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-FFRep1-BinA-PCRrep1_S22_R2_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI1754XQJY/",
"accession": "IGVFFI1754XQJY",
"aliases": [
"jesse-engreitz:220228_8merInsertion-THP1-Amp_PPIF_promoter-BioRep4-FFrep1-BinA-PCRrep1_R1"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2023-12-05T18:31:56.954189+00:00",
"file_format": "fastq",
"file_size": 8297660,
"href": "/sequence-files/IGVFFI1754XQJY/@@download/IGVFFI1754XQJY.fastq.gz",
"md5sum": "ed648d5891983689df943be61e847c55",
"s3_uri": "s3://igvf-files/2023/12/05/df189db9-0f02-4ab7-af73-0a172e50c226/IGVFFI1754XQJY.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-FFRep1-BinA-PCRrep1_S22_R1_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI6561JCKT/",
"accession": "IGVFFI6561JCKT",
"aliases": [
"jesse-engreitz:220228_8merInsertion-THP1-Amp_PPIF_promoter-BioRep4-FFrep1-BinA-PCRrep2_R2"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2023-12-05T18:51:03.471091+00:00",
"file_format": "fastq",
"file_size": 16934192,
"href": "/sequence-files/IGVFFI6561JCKT/@@download/IGVFFI6561JCKT.fastq.gz",
"md5sum": "b62fd606181019e39f62c64a7eb1c91e",
"s3_uri": "s3://igvf-files/2023/12/05/9a7dc0e9-9fb8-491f-8632-409125ed0f54/IGVFFI6561JCKT.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-FFRep1-BinA-PCRrep2_S118_R2_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI7214MLEI/",
"accession": "IGVFFI7214MLEI",
"aliases": [
"jesse-engreitz:220228_8merInsertion-THP1-Amp_PPIF_promoter-BioRep4-FFrep1-BinA-PCRrep2_R1"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2023-12-05T18:38:12.500203+00:00",
"file_format": "fastq",
"file_size": 8638572,
"href": "/sequence-files/IGVFFI7214MLEI/@@download/IGVFFI7214MLEI.fastq.gz",
"md5sum": "c68aadb5e816ee188cd9236c66e4c268",
"s3_uri": "s3://igvf-files/2023/12/05/c9cc2b35-53ae-4034-b834-66c9c1c75938/IGVFFI7214MLEI.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-FFRep1-BinA-PCRrep2_S118_R1_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI0797YDWG/",
"accession": "IGVFFI0797YDWG",
"aliases": [
"jesse-engreitz:220228_8merInsertion-THP1-Amp_PPIF_promoter-BioRep4-FFrep1-BinA-PCRrep1_I2"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2023-12-05T19:09:49.565982+00:00",
"file_format": "fastq",
"file_size": 2646013,
"href": "/sequence-files/IGVFFI0797YDWG/@@download/IGVFFI0797YDWG.fastq.gz",
"md5sum": "110bb619c887e1ff681237cb834748a8",
"s3_uri": "s3://igvf-files/2023/12/05/c3f0fff2-37b3-49d9-bc64-393b5e402082/IGVFFI0797YDWG.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-FFRep1-BinA-PCRrep1_S22_I2_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI3543WVWH/",
"accession": "IGVFFI3543WVWH",
"aliases": [
"jesse-engreitz:220228_8merInsertion-THP1-Amp_PPIF_promoter-BioRep4-FFrep1-BinA-PCRrep2_I1"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2023-12-05T19:03:44.809005+00:00",
"file_format": "fastq",
"file_size": 2905512,
"href": "/sequence-files/IGVFFI3543WVWH/@@download/IGVFFI3543WVWH.fastq.gz",
"md5sum": "aeca52b75645f3f22003048017a41239",
"s3_uri": "s3://igvf-files/2023/12/05/caae6973-9fda-4093-966c-fcbe030527b8/IGVFFI3543WVWH.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-FFRep1-BinA-PCRrep2_S118_I1_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI3594OXIX/",
"accession": "IGVFFI3594OXIX",
"aliases": [
"jesse-engreitz:220228_8merInsertion-THP1-Amp_PPIF_promoter-BioRep4-FFrep1-BinA-PCRrep1_I1"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2023-12-05T18:57:23.221022+00:00",
"file_format": "fastq",
"file_size": 2767925,
"href": "/sequence-files/IGVFFI3594OXIX/@@download/IGVFFI3594OXIX.fastq.gz",
"md5sum": "7e32138509fa0ae18ec9948dc7bb409f",
"s3_uri": "s3://igvf-files/2023/12/05/6b914c90-c742-47c6-8826-2f47e5329e55/IGVFFI3594OXIX.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-FFRep1-BinA-PCRrep1_S22_I1_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI6830NYRY/",
"accession": "IGVFFI6830NYRY",
"aliases": [
"jesse-engreitz:220228_8merInsertion-THP1-Amp_PPIF_promoter-BioRep4-FFrep1-BinA-PCRrep2_I2"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2023-12-05T19:16:00.217899+00:00",
"file_format": "fastq",
"file_size": 2807414,
"href": "/sequence-files/IGVFFI6830NYRY/@@download/IGVFFI6830NYRY.fastq.gz",
"md5sum": "ce9b429c605999875d4e01071549eec9",
"s3_uri": "s3://igvf-files/2023/12/05/72991e34-dc0a-4083-aa27-50adee46ad5e/IGVFFI6830NYRY.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-FFRep1-BinA-PCRrep2_S118_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": "2023-12-20T23:09:56.765064+00:00",
"samples": [
{
"@id": "/in-vitro-systems/IGVFSM7338BXZP/",
"@type": [
"InVitroSystem",
"Biosample",
"Sample",
"Item"
],
"accession": "IGVFSM7338BXZP",
"aliases": [
"jesse-engreitz:220228_8merInsertion-THP1-Amp_PPIF_promoter-BioRep4-FFrep1-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": "2023-12-05T18:31:56.954189+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": "5ac81414-7836-4a3e-8abd-2a5daf76a2f5"
}