{
"@context": "/terms/",
"@id": "/measurement-sets/IGVFDS9920OIUA/",
"@type": [
"MeasurementSet",
"FileSet",
"Item"
],
"accession": "IGVFDS9920OIUA",
"aliases": [
"jesse-engreitz:220228_8merInsertion-THP1-Amp_PPIF_promoter-BioRep2-FFrep1-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 [IGVFSM1147YJAE](/in-vitro-systems/IGVFSM1147YJAE/) 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/IGVFSM1147YJAE/"
},
{
"category": "missing publication",
"detail": "In vitro system [IGVFSM1147YJAE](/in-vitro-systems/IGVFSM1147YJAE/) 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/IGVFSM1147YJAE/"
},
{
"category": "missing publication",
"detail": "Measurement set [IGVFDS9920OIUA](/measurement-sets/IGVFDS9920OIUA/) 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/IGVFDS9920OIUA/"
},
{
"category": "missing sequencing kit",
"detail": "Measurement set [IGVFDS9920OIUA](/measurement-sets/IGVFDS9920OIUA/) has sequence file(s) [IGVFFI7915UMXY](/sequence-files/IGVFFI7915UMXY/), [IGVFFI2308XQRE](/sequence-files/IGVFFI2308XQRE/), [IGVFFI4903GCYN](/sequence-files/IGVFFI4903GCYN/), [IGVFFI6692LVQH](/sequence-files/IGVFFI6692LVQH/), [IGVFFI6547BNBI](/sequence-files/IGVFFI6547BNBI/), [IGVFFI5450VTQL](/sequence-files/IGVFFI5450VTQL/), [IGVFFI3377HFWV](/sequence-files/IGVFFI3377HFWV/), [IGVFFI1896YLEZ](/sequence-files/IGVFFI1896YLEZ/) 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/IGVFDS9920OIUA/"
},
{
"category": "missing sequence specification",
"detail": "Measurement set [IGVFDS9920OIUA](/measurement-sets/IGVFDS9920OIUA/) has sequence file(s): [IGVFFI7915UMXY](/sequence-files/IGVFFI7915UMXY/), [IGVFFI2308XQRE](/sequence-files/IGVFFI2308XQRE/), [IGVFFI4903GCYN](/sequence-files/IGVFFI4903GCYN/), [IGVFFI6692LVQH](/sequence-files/IGVFFI6692LVQH/), [IGVFFI6547BNBI](/sequence-files/IGVFFI6547BNBI/), [IGVFFI5450VTQL](/sequence-files/IGVFFI5450VTQL/), [IGVFFI3377HFWV](/sequence-files/IGVFFI3377HFWV/), [IGVFFI1896YLEZ](/sequence-files/IGVFFI1896YLEZ/) 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/IGVFDS9920OIUA/"
}
],
"WARNING": [
{
"category": "missing auxiliary set",
"detail": "Measurement set [IGVFDS9920OIUA](/measurement-sets/IGVFDS9920OIUA/) 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/IGVFDS9920OIUA/"
}
]
},
"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": "2023-11-30T22:46:12.279619+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": [
{
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"accession": "IGVFFI7915UMXY",
"aliases": [
"jesse-engreitz:220228_8merInsertion-THP1-Amp_PPIF_promoter-BioRep2-FFrep1-BinD-PCRrep2_R2"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2023-12-05T18:45:31.122612+00:00",
"file_format": "fastq",
"file_size": 75700191,
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"md5sum": "0cfea90a7b539e97b55bf7bcd791db10",
"s3_uri": "s3://igvf-files/2023/12/05/9a2f31fe-4cd5-4614-9de8-6d73fe9f3b9b/IGVFFI7915UMXY.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-BinD_R2_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI2308XQRE/",
"accession": "IGVFFI2308XQRE",
"aliases": [
"jesse-engreitz:220228_8merInsertion-THP1-Amp_PPIF_promoter-BioRep2-FFrep1-BinD-PCRrep2_R1"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2023-12-05T18:33:31.322128+00:00",
"file_format": "fastq",
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"href": "/sequence-files/IGVFFI2308XQRE/@@download/IGVFFI2308XQRE.fastq.gz",
"md5sum": "dc6ff6507ca77bb6f430442c322a1044",
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"sequencing_platform": {
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"status": "released",
"term_name": "Illumina NextSeq 550"
},
"status": "released",
"submitted_file_name": "220228pPPIF-FFSample-6-D21-pPPIF-Amp-pPPIF-2-1-2-BinD_R1_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI4903GCYN/",
"accession": "IGVFFI4903GCYN",
"aliases": [
"jesse-engreitz:220228_8merInsertion-THP1-Amp_PPIF_promoter-BioRep2-FFrep1-BinD-PCRrep1_I2"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2023-12-05T19:02:20.704528+00:00",
"file_format": "fastq",
"file_size": 12596118,
"href": "/sequence-files/IGVFFI4903GCYN/@@download/IGVFFI4903GCYN.fastq.gz",
"md5sum": "fbda45ac5b3772b9a346f355dbcb2f4a",
"s3_uri": "s3://igvf-files/2023/12/05/e7b0c930-2524-4797-bdb5-2ba9820c5207/IGVFFI4903GCYN.fastq.gz",
"sequencing_platform": {
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"status": "released",
"term_name": "Illumina NextSeq 550"
},
"status": "released",
"submitted_file_name": "220228pPPIF-FFSample-6-D21-pPPIF-Amp-pPPIF-2-1-1-BinD_I2_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI6692LVQH/",
"accession": "IGVFFI6692LVQH",
"aliases": [
"jesse-engreitz:220228_8merInsertion-THP1-Amp_PPIF_promoter-BioRep2-FFrep1-BinD-PCRrep2_I1"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2023-12-05T18:56:49.033571+00:00",
"file_format": "fastq",
"file_size": 16075060,
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"md5sum": "1c257dd069be3c9a41347a22ed6e41f5",
"s3_uri": "s3://igvf-files/2023/12/05/836c1338-9376-4c59-8b59-4baea5565a18/IGVFFI6692LVQH.fastq.gz",
"sequencing_platform": {
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"status": "released",
"term_name": "Illumina NextSeq 550"
},
"status": "released",
"submitted_file_name": "220228pPPIF-FFSample-6-D21-pPPIF-Amp-pPPIF-2-1-2-BinD_I1_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI6547BNBI/",
"accession": "IGVFFI6547BNBI",
"aliases": [
"jesse-engreitz:220228_8merInsertion-THP1-Amp_PPIF_promoter-BioRep2-FFrep1-BinD-PCRrep1_I1"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2023-12-05T18:51:06.042966+00:00",
"file_format": "fastq",
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"md5sum": "4490f0cc458d73a19e1c3cfc1ad8d1f2",
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"sequencing_platform": {
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"status": "released",
"term_name": "Illumina NextSeq 550"
},
"status": "released",
"submitted_file_name": "220228pPPIF-FFSample-6-D21-pPPIF-Amp-pPPIF-2-1-1-BinD_I1_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI5450VTQL/",
"accession": "IGVFFI5450VTQL",
"aliases": [
"jesse-engreitz:220228_8merInsertion-THP1-Amp_PPIF_promoter-BioRep2-FFrep1-BinD-PCRrep2_I2"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2023-12-05T19:07:55.161654+00:00",
"file_format": "fastq",
"file_size": 14276397,
"href": "/sequence-files/IGVFFI5450VTQL/@@download/IGVFFI5450VTQL.fastq.gz",
"md5sum": "dd1b07f5fb295a804b5d428c8444547f",
"s3_uri": "s3://igvf-files/2023/12/05/9063b750-5125-4cb7-8d94-3a82065ebdbd/IGVFFI5450VTQL.fastq.gz",
"sequencing_platform": {
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"status": "released",
"term_name": "Illumina NextSeq 550"
},
"status": "released",
"submitted_file_name": "220228pPPIF-FFSample-6-D21-pPPIF-Amp-pPPIF-2-1-2-BinD_I2_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI3377HFWV/",
"accession": "IGVFFI3377HFWV",
"aliases": [
"jesse-engreitz:220228_8merInsertion-THP1-Amp_PPIF_promoter-BioRep2-FFrep1-BinD-PCRrep1_R2"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2023-12-05T18:39:29.002714+00:00",
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"md5sum": "c83552a9dcf32a7f7685f3f1680741be",
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"sequencing_platform": {
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"term_name": "Illumina NextSeq 550"
},
"status": "released",
"submitted_file_name": "220228pPPIF-FFSample-6-D21-pPPIF-Amp-pPPIF-2-1-1-BinD_R2_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI1896YLEZ/",
"accession": "IGVFFI1896YLEZ",
"aliases": [
"jesse-engreitz:220228_8merInsertion-THP1-Amp_PPIF_promoter-BioRep2-FFrep1-BinD-PCRrep1_R1"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2023-12-05T18:27:47.683115+00:00",
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"md5sum": "bb351d1b61f6d9995595786696843281",
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"sequencing_platform": {
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"status": "released",
"term_name": "Illumina NextSeq 550"
},
"status": "released",
"submitted_file_name": "220228pPPIF-FFSample-6-D21-pPPIF-Amp-pPPIF-2-1-1-BinD_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": "2023-12-20T23:09:54.334944+00:00",
"samples": [
{
"@id": "/in-vitro-systems/IGVFSM1147YJAE/",
"@type": [
"InVitroSystem",
"Biosample",
"Sample",
"Item"
],
"accession": "IGVFSM1147YJAE",
"aliases": [
"jesse-engreitz:220228_8merInsertion-THP1-Amp_PPIF_promoter-BioRep2-FFrep1-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": "2023-12-05T18:27:47.683115+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": "5a940e07-2b7e-4a49-8566-97553bb832c8"
}