{
"@context": "/terms/",
"@id": "/measurement-sets/IGVFDS1646OXQU/",
"@type": [
"MeasurementSet",
"FileSet",
"Item"
],
"accession": "IGVFDS1646OXQU",
"aliases": [
"jesse-engreitz:230807S022-THP1-P153-Amp_PPIF_promoter-BioRep1-FFrep4-BinB_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 [IGVFDS1646OXQU](/measurement-sets/IGVFDS1646OXQU/) 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/IGVFDS1646OXQU/"
},
{
"category": "missing sequencing kit",
"detail": "Measurement set [IGVFDS1646OXQU](/measurement-sets/IGVFDS1646OXQU/) has sequence file(s) [IGVFFI1769UJZW](/sequence-files/IGVFFI1769UJZW/), [IGVFFI3901KYJF](/sequence-files/IGVFFI3901KYJF/), [IGVFFI4810KDFS](/sequence-files/IGVFFI4810KDFS/), [IGVFFI9549SHBR](/sequence-files/IGVFFI9549SHBR/), [IGVFFI6619HXFY](/sequence-files/IGVFFI6619HXFY/), [IGVFFI0822ARHF](/sequence-files/IGVFFI0822ARHF/), [IGVFFI8159BBLG](/sequence-files/IGVFFI8159BBLG/), [IGVFFI7860CKDG](/sequence-files/IGVFFI7860CKDG/), [IGVFFI2805ZHPD](/sequence-files/IGVFFI2805ZHPD/), [IGVFFI9755LYIY](/sequence-files/IGVFFI9755LYIY/), [IGVFFI3036QBLG](/sequence-files/IGVFFI3036QBLG/), [IGVFFI5314KIVP](/sequence-files/IGVFFI5314KIVP/), [IGVFFI3618TRFU](/sequence-files/IGVFFI3618TRFU/), [IGVFFI5586ISBW](/sequence-files/IGVFFI5586ISBW/), [IGVFFI7288DVFW](/sequence-files/IGVFFI7288DVFW/), [IGVFFI1882RXDV](/sequence-files/IGVFFI1882RXDV/), [IGVFFI3430YNMZ](/sequence-files/IGVFFI3430YNMZ/), [IGVFFI2287AMTP](/sequence-files/IGVFFI2287AMTP/), [IGVFFI7587CEAL](/sequence-files/IGVFFI7587CEAL/), [IGVFFI0770IPCR](/sequence-files/IGVFFI0770IPCR/), [IGVFFI7505JZEL](/sequence-files/IGVFFI7505JZEL/), [IGVFFI7936VWTK](/sequence-files/IGVFFI7936VWTK/), [IGVFFI0244ZFKA](/sequence-files/IGVFFI0244ZFKA/), [IGVFFI4676NMAM](/sequence-files/IGVFFI4676NMAM/), [IGVFFI5230OUBN](/sequence-files/IGVFFI5230OUBN/), [IGVFFI7983ZPMM](/sequence-files/IGVFFI7983ZPMM/), [IGVFFI9923KKAW](/sequence-files/IGVFFI9923KKAW/), [IGVFFI2362YMIY](/sequence-files/IGVFFI2362YMIY/), [IGVFFI1751WHIG](/sequence-files/IGVFFI1751WHIG/), [IGVFFI8293WVYF](/sequence-files/IGVFFI8293WVYF/), [IGVFFI0375RQTR](/sequence-files/IGVFFI0375RQTR/), [IGVFFI6936ODZR](/sequence-files/IGVFFI6936ODZR/), [IGVFFI8913KWZS](/sequence-files/IGVFFI8913KWZS/), [IGVFFI0536STQM](/sequence-files/IGVFFI0536STQM/), [IGVFFI8270ARRR](/sequence-files/IGVFFI8270ARRR/), [IGVFFI9066NZWE](/sequence-files/IGVFFI9066NZWE/), [IGVFFI0415KZAZ](/sequence-files/IGVFFI0415KZAZ/), [IGVFFI6850GEDM](/sequence-files/IGVFFI6850GEDM/), [IGVFFI9114AVWK](/sequence-files/IGVFFI9114AVWK/), [IGVFFI6121CAKN](/sequence-files/IGVFFI6121CAKN/), [IGVFFI2180EYJI](/sequence-files/IGVFFI2180EYJI/), [IGVFFI0516KOIJ](/sequence-files/IGVFFI0516KOIJ/), [IGVFFI5025DAYH](/sequence-files/IGVFFI5025DAYH/), [IGVFFI8573ZDPU](/sequence-files/IGVFFI8573ZDPU/), [IGVFFI4047ZMCC](/sequence-files/IGVFFI4047ZMCC/), [IGVFFI6752CCWW](/sequence-files/IGVFFI6752CCWW/), [IGVFFI6273IBMR](/sequence-files/IGVFFI6273IBMR/), [IGVFFI9672LAWY](/sequence-files/IGVFFI9672LAWY/) 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/IGVFDS1646OXQU/"
},
{
"category": "missing sequence specification",
"detail": "Measurement set [IGVFDS1646OXQU](/measurement-sets/IGVFDS1646OXQU/) has sequence file(s): [IGVFFI1769UJZW](/sequence-files/IGVFFI1769UJZW/), [IGVFFI3901KYJF](/sequence-files/IGVFFI3901KYJF/), [IGVFFI4810KDFS](/sequence-files/IGVFFI4810KDFS/), [IGVFFI9549SHBR](/sequence-files/IGVFFI9549SHBR/), [IGVFFI6619HXFY](/sequence-files/IGVFFI6619HXFY/), [IGVFFI0822ARHF](/sequence-files/IGVFFI0822ARHF/), [IGVFFI8159BBLG](/sequence-files/IGVFFI8159BBLG/), [IGVFFI7860CKDG](/sequence-files/IGVFFI7860CKDG/), [IGVFFI2805ZHPD](/sequence-files/IGVFFI2805ZHPD/), [IGVFFI9755LYIY](/sequence-files/IGVFFI9755LYIY/), [IGVFFI3036QBLG](/sequence-files/IGVFFI3036QBLG/), [IGVFFI5314KIVP](/sequence-files/IGVFFI5314KIVP/), [IGVFFI3618TRFU](/sequence-files/IGVFFI3618TRFU/), [IGVFFI5586ISBW](/sequence-files/IGVFFI5586ISBW/), [IGVFFI7288DVFW](/sequence-files/IGVFFI7288DVFW/), [IGVFFI1882RXDV](/sequence-files/IGVFFI1882RXDV/), [IGVFFI3430YNMZ](/sequence-files/IGVFFI3430YNMZ/), [IGVFFI2287AMTP](/sequence-files/IGVFFI2287AMTP/), [IGVFFI7587CEAL](/sequence-files/IGVFFI7587CEAL/), [IGVFFI0770IPCR](/sequence-files/IGVFFI0770IPCR/), [IGVFFI7505JZEL](/sequence-files/IGVFFI7505JZEL/), [IGVFFI7936VWTK](/sequence-files/IGVFFI7936VWTK/), [IGVFFI0244ZFKA](/sequence-files/IGVFFI0244ZFKA/), [IGVFFI4676NMAM](/sequence-files/IGVFFI4676NMAM/), [IGVFFI5230OUBN](/sequence-files/IGVFFI5230OUBN/), [IGVFFI7983ZPMM](/sequence-files/IGVFFI7983ZPMM/), [IGVFFI9923KKAW](/sequence-files/IGVFFI9923KKAW/), [IGVFFI2362YMIY](/sequence-files/IGVFFI2362YMIY/), [IGVFFI1751WHIG](/sequence-files/IGVFFI1751WHIG/), [IGVFFI8293WVYF](/sequence-files/IGVFFI8293WVYF/), [IGVFFI0375RQTR](/sequence-files/IGVFFI0375RQTR/), [IGVFFI6936ODZR](/sequence-files/IGVFFI6936ODZR/), [IGVFFI8913KWZS](/sequence-files/IGVFFI8913KWZS/), [IGVFFI0536STQM](/sequence-files/IGVFFI0536STQM/), [IGVFFI8270ARRR](/sequence-files/IGVFFI8270ARRR/), [IGVFFI9066NZWE](/sequence-files/IGVFFI9066NZWE/), [IGVFFI0415KZAZ](/sequence-files/IGVFFI0415KZAZ/), [IGVFFI6850GEDM](/sequence-files/IGVFFI6850GEDM/), [IGVFFI9114AVWK](/sequence-files/IGVFFI9114AVWK/), [IGVFFI6121CAKN](/sequence-files/IGVFFI6121CAKN/), [IGVFFI2180EYJI](/sequence-files/IGVFFI2180EYJI/), [IGVFFI0516KOIJ](/sequence-files/IGVFFI0516KOIJ/), [IGVFFI5025DAYH](/sequence-files/IGVFFI5025DAYH/), [IGVFFI8573ZDPU](/sequence-files/IGVFFI8573ZDPU/), [IGVFFI4047ZMCC](/sequence-files/IGVFFI4047ZMCC/), [IGVFFI6752CCWW](/sequence-files/IGVFFI6752CCWW/), [IGVFFI6273IBMR](/sequence-files/IGVFFI6273IBMR/), [IGVFFI9672LAWY](/sequence-files/IGVFFI9672LAWY/) 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/IGVFDS1646OXQU/"
},
{
"category": "mismatched status",
"detail": "Released in vitro system [IGVFSM8031IIWI](/in-vitro-systems/IGVFSM8031IIWI/) has in progress subobject construct library set [IGVFDS6982DESN](/construct-library-sets/IGVFDS6982DESN/).",
"level": 30,
"level_name": "INTERNAL_ACTION",
"name": "audit_item_status",
"path": "/in-vitro-systems/IGVFSM8031IIWI/"
},
{
"category": "missing publication",
"detail": "In vitro system [IGVFSM8031IIWI](/in-vitro-systems/IGVFSM8031IIWI/) 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/IGVFSM8031IIWI/"
}
],
"WARNING": [
{
"category": "missing auxiliary set",
"detail": "Measurement set [IGVFDS1646OXQU](/measurement-sets/IGVFDS1646OXQU/) 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/IGVFDS1646OXQU/"
}
]
},
"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/IGVFDS6982DESN/",
"accession": "IGVFDS6982DESN",
"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/IGVFDS5864UGFT/",
"accession": "IGVFDS5864UGFT",
"aliases": [
"jesse-engreitz:230807S022-THP1-P153-Amp_PPIF_promoter-THP1-PE2_Exp2_NegControl_AmpliconSequencing"
],
"status": "released"
}
],
"control_for": [],
"creation_timestamp": "2023-11-30T22:49:49.031384+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/IGVFFI1769UJZW/",
"accession": "IGVFFI1769UJZW",
"aliases": [
"jesse-engreitz:230807S022-THP1-P153-Amp_PPIF_promoter-BioRep1-FFrep4-BinB-PCRrep6_I2"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2023-12-05T21:14:41.491202+00:00",
"file_format": "fastq",
"file_size": 1922269,
"href": "/sequence-files/IGVFFI1769UJZW/@@download/IGVFFI1769UJZW.fastq.gz",
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"sequencing_platform": {
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"status": "released",
"term_name": "Illumina NextSeq 550"
},
"status": "released",
"submitted_file_name": "230807S022-THP1-P153-Amp_PPIF_promoter-BioRep1-FFrep4-BinB-PCRrep6_S162_I2_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI3901KYJF/",
"accession": "IGVFFI3901KYJF",
"aliases": [
"jesse-engreitz:230807S022-THP1-P153-Amp_PPIF_promoter-BioRep1-FFrep4-BinB-PCRrep11_R2"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2023-12-05T21:11:28.461416+00:00",
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"file_size": 6982008,
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"status": "released",
"term_name": "Illumina NextSeq 550"
},
"status": "released",
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"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI4810KDFS/",
"accession": "IGVFFI4810KDFS",
"aliases": [
"jesse-engreitz:230807S022-THP1-P153-Amp_PPIF_promoter-BioRep1-FFrep4-BinB-PCRrep5_I1"
],
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"status": "released",
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},
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"upload_status": "validated"
},
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"accession": "IGVFFI9549SHBR",
"aliases": [
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],
"content_type": "reads",
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},
"status": "released",
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"upload_status": "validated"
},
{
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"accession": "IGVFFI6619HXFY",
"aliases": [
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],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2023-12-05T21:16:45.070227+00:00",
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},
"status": "released",
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"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI0822ARHF/",
"accession": "IGVFFI0822ARHF",
"aliases": [
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],
"content_type": "reads",
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},
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},
{
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],
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},
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"upload_status": "validated"
},
{
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"aliases": [
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],
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},
"status": "released",
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"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI2805ZHPD/",
"accession": "IGVFFI2805ZHPD",
"aliases": [
"jesse-engreitz:230807S022-THP1-P153-Amp_PPIF_promoter-BioRep1-FFrep4-BinB-PCRrep11_R1"
],
"content_type": "reads",
"controlled_access": false,
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"status": "released",
"term_name": "Illumina NextSeq 550"
},
"status": "released",
"submitted_file_name": "230807S022-THP1-P153-Amp_PPIF_promoter-BioRep1-FFrep4-BinB-PCRrep11_S167_R1_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI9755LYIY/",
"accession": "IGVFFI9755LYIY",
"aliases": [
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],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2023-12-05T21:13:22.221888+00:00",
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"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI9672LAWY/",
"accession": "IGVFFI9672LAWY",
"aliases": [
"jesse-engreitz:230807S022-THP1-P153-Amp_PPIF_promoter-BioRep1-FFrep4-BinB-PCRrep8_I2"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2023-12-05T21:15:52.182596+00:00",
"file_format": "fastq",
"file_size": 1802653,
"href": "/sequence-files/IGVFFI9672LAWY/@@download/IGVFFI9672LAWY.fastq.gz",
"md5sum": "ee9c642138174a0af7574a626c906a7e",
"s3_uri": "s3://igvf-files/2023/12/05/3613826f-c8b5-4aec-9799-9e14a445e141/IGVFFI9672LAWY.fastq.gz",
"sequencing_platform": {
"@id": "/platform-terms/EFO_0008566/",
"status": "released",
"term_name": "Illumina NextSeq 550"
},
"status": "released",
"submitted_file_name": "230807S022-THP1-P153-Amp_PPIF_promoter-BioRep1-FFrep4-BinB-PCRrep8_S164_I2_001.fastq.gz",
"upload_status": "validated"
}
],
"input_for": [
"/analysis-sets/IGVFDS3423PSID/"
],
"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": "2023-12-20T23:06:11.718935+00:00",
"samples": [
{
"@id": "/in-vitro-systems/IGVFSM8031IIWI/",
"@type": [
"InVitroSystem",
"Biosample",
"Sample",
"Item"
],
"accession": "IGVFSM8031IIWI",
"aliases": [
"jesse-engreitz:230807S022-THP1-P153-Amp_PPIF_promoter-BioRep1-FFrep4-BinB"
],
"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 26-50% 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": "2023-12-05T21:09:52.245558+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": "03ed455f-e888-4db6-b933-8acf66616d50"
}