{
"@context": "/terms/",
"@id": "/measurement-sets/IGVFDS1327XCCU/",
"@type": [
"MeasurementSet",
"FileSet",
"Item"
],
"accession": "IGVFDS1327XCCU",
"aliases": [
"jesse-engreitz:230807S022-THP1-P153-Amp_PPIF_promoter-BioRep2-FFrep3-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 [IGVFSM5844KEUJ](/in-vitro-systems/IGVFSM5844KEUJ/) 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/IGVFSM5844KEUJ/"
},
{
"category": "missing publication",
"detail": "In vitro system [IGVFSM5844KEUJ](/in-vitro-systems/IGVFSM5844KEUJ/) 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/IGVFSM5844KEUJ/"
},
{
"category": "missing publication",
"detail": "Measurement set [IGVFDS1327XCCU](/measurement-sets/IGVFDS1327XCCU/) 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/IGVFDS1327XCCU/"
},
{
"category": "missing sequencing kit",
"detail": "Measurement set [IGVFDS1327XCCU](/measurement-sets/IGVFDS1327XCCU/) has sequence file(s) [IGVFFI3781UEFZ](/sequence-files/IGVFFI3781UEFZ/), [IGVFFI1078IQWD](/sequence-files/IGVFFI1078IQWD/), [IGVFFI0174HPHA](/sequence-files/IGVFFI0174HPHA/), [IGVFFI4807AAZI](/sequence-files/IGVFFI4807AAZI/), [IGVFFI6312OYBZ](/sequence-files/IGVFFI6312OYBZ/), [IGVFFI2554OOEP](/sequence-files/IGVFFI2554OOEP/), [IGVFFI2217TFSA](/sequence-files/IGVFFI2217TFSA/), [IGVFFI8870KVMB](/sequence-files/IGVFFI8870KVMB/), [IGVFFI6612TAEI](/sequence-files/IGVFFI6612TAEI/), [IGVFFI5180CXKH](/sequence-files/IGVFFI5180CXKH/), [IGVFFI0555LQIR](/sequence-files/IGVFFI0555LQIR/), [IGVFFI1656CXSA](/sequence-files/IGVFFI1656CXSA/), [IGVFFI5278LQAY](/sequence-files/IGVFFI5278LQAY/), [IGVFFI9429JMOJ](/sequence-files/IGVFFI9429JMOJ/), [IGVFFI5534AWYJ](/sequence-files/IGVFFI5534AWYJ/), [IGVFFI5267KVMQ](/sequence-files/IGVFFI5267KVMQ/), [IGVFFI6079ATVH](/sequence-files/IGVFFI6079ATVH/), [IGVFFI8745VLNT](/sequence-files/IGVFFI8745VLNT/), [IGVFFI2727WQVS](/sequence-files/IGVFFI2727WQVS/), [IGVFFI2303HBSE](/sequence-files/IGVFFI2303HBSE/), [IGVFFI7121SZJD](/sequence-files/IGVFFI7121SZJD/), [IGVFFI3043STQW](/sequence-files/IGVFFI3043STQW/), [IGVFFI6401MICT](/sequence-files/IGVFFI6401MICT/), [IGVFFI9742SYME](/sequence-files/IGVFFI9742SYME/), [IGVFFI4785RSVU](/sequence-files/IGVFFI4785RSVU/), [IGVFFI6399PGJQ](/sequence-files/IGVFFI6399PGJQ/), [IGVFFI9518UFDV](/sequence-files/IGVFFI9518UFDV/), [IGVFFI9207IDMM](/sequence-files/IGVFFI9207IDMM/), [IGVFFI4924BALH](/sequence-files/IGVFFI4924BALH/), [IGVFFI0354AZOM](/sequence-files/IGVFFI0354AZOM/), [IGVFFI0018FVXE](/sequence-files/IGVFFI0018FVXE/), [IGVFFI3066LWHM](/sequence-files/IGVFFI3066LWHM/), [IGVFFI7747ROLT](/sequence-files/IGVFFI7747ROLT/), [IGVFFI6306UCPY](/sequence-files/IGVFFI6306UCPY/), [IGVFFI3793DPQT](/sequence-files/IGVFFI3793DPQT/), [IGVFFI0071ZIGG](/sequence-files/IGVFFI0071ZIGG/), [IGVFFI5607TJVZ](/sequence-files/IGVFFI5607TJVZ/), [IGVFFI8883LRBT](/sequence-files/IGVFFI8883LRBT/), [IGVFFI3609QXCK](/sequence-files/IGVFFI3609QXCK/), [IGVFFI5747LSNL](/sequence-files/IGVFFI5747LSNL/), [IGVFFI6997XITK](/sequence-files/IGVFFI6997XITK/), [IGVFFI6213BYUY](/sequence-files/IGVFFI6213BYUY/), [IGVFFI5168KASR](/sequence-files/IGVFFI5168KASR/), [IGVFFI7350UQLW](/sequence-files/IGVFFI7350UQLW/), [IGVFFI7338DWWK](/sequence-files/IGVFFI7338DWWK/), [IGVFFI0938WPJU](/sequence-files/IGVFFI0938WPJU/), [IGVFFI3101HSEU](/sequence-files/IGVFFI3101HSEU/), [IGVFFI3329KNCB](/sequence-files/IGVFFI3329KNCB/) 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/IGVFDS1327XCCU/"
},
{
"category": "missing sequence specification",
"detail": "Measurement set [IGVFDS1327XCCU](/measurement-sets/IGVFDS1327XCCU/) has sequence file(s): [IGVFFI3781UEFZ](/sequence-files/IGVFFI3781UEFZ/), [IGVFFI1078IQWD](/sequence-files/IGVFFI1078IQWD/), [IGVFFI0174HPHA](/sequence-files/IGVFFI0174HPHA/), [IGVFFI4807AAZI](/sequence-files/IGVFFI4807AAZI/), [IGVFFI6312OYBZ](/sequence-files/IGVFFI6312OYBZ/), [IGVFFI2554OOEP](/sequence-files/IGVFFI2554OOEP/), [IGVFFI2217TFSA](/sequence-files/IGVFFI2217TFSA/), [IGVFFI8870KVMB](/sequence-files/IGVFFI8870KVMB/), [IGVFFI6612TAEI](/sequence-files/IGVFFI6612TAEI/), [IGVFFI5180CXKH](/sequence-files/IGVFFI5180CXKH/), [IGVFFI0555LQIR](/sequence-files/IGVFFI0555LQIR/), [IGVFFI1656CXSA](/sequence-files/IGVFFI1656CXSA/), [IGVFFI5278LQAY](/sequence-files/IGVFFI5278LQAY/), [IGVFFI9429JMOJ](/sequence-files/IGVFFI9429JMOJ/), [IGVFFI5534AWYJ](/sequence-files/IGVFFI5534AWYJ/), [IGVFFI5267KVMQ](/sequence-files/IGVFFI5267KVMQ/), [IGVFFI6079ATVH](/sequence-files/IGVFFI6079ATVH/), [IGVFFI8745VLNT](/sequence-files/IGVFFI8745VLNT/), [IGVFFI2727WQVS](/sequence-files/IGVFFI2727WQVS/), [IGVFFI2303HBSE](/sequence-files/IGVFFI2303HBSE/), [IGVFFI7121SZJD](/sequence-files/IGVFFI7121SZJD/), [IGVFFI3043STQW](/sequence-files/IGVFFI3043STQW/), [IGVFFI6401MICT](/sequence-files/IGVFFI6401MICT/), [IGVFFI9742SYME](/sequence-files/IGVFFI9742SYME/), [IGVFFI4785RSVU](/sequence-files/IGVFFI4785RSVU/), [IGVFFI6399PGJQ](/sequence-files/IGVFFI6399PGJQ/), [IGVFFI9518UFDV](/sequence-files/IGVFFI9518UFDV/), [IGVFFI9207IDMM](/sequence-files/IGVFFI9207IDMM/), [IGVFFI4924BALH](/sequence-files/IGVFFI4924BALH/), [IGVFFI0354AZOM](/sequence-files/IGVFFI0354AZOM/), [IGVFFI0018FVXE](/sequence-files/IGVFFI0018FVXE/), [IGVFFI3066LWHM](/sequence-files/IGVFFI3066LWHM/), [IGVFFI7747ROLT](/sequence-files/IGVFFI7747ROLT/), [IGVFFI6306UCPY](/sequence-files/IGVFFI6306UCPY/), [IGVFFI3793DPQT](/sequence-files/IGVFFI3793DPQT/), [IGVFFI0071ZIGG](/sequence-files/IGVFFI0071ZIGG/), [IGVFFI5607TJVZ](/sequence-files/IGVFFI5607TJVZ/), [IGVFFI8883LRBT](/sequence-files/IGVFFI8883LRBT/), [IGVFFI3609QXCK](/sequence-files/IGVFFI3609QXCK/), [IGVFFI5747LSNL](/sequence-files/IGVFFI5747LSNL/), [IGVFFI6997XITK](/sequence-files/IGVFFI6997XITK/), [IGVFFI6213BYUY](/sequence-files/IGVFFI6213BYUY/), [IGVFFI5168KASR](/sequence-files/IGVFFI5168KASR/), [IGVFFI7350UQLW](/sequence-files/IGVFFI7350UQLW/), [IGVFFI7338DWWK](/sequence-files/IGVFFI7338DWWK/), [IGVFFI0938WPJU](/sequence-files/IGVFFI0938WPJU/), [IGVFFI3101HSEU](/sequence-files/IGVFFI3101HSEU/), [IGVFFI3329KNCB](/sequence-files/IGVFFI3329KNCB/) 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/IGVFDS1327XCCU/"
}
],
"WARNING": [
{
"category": "missing auxiliary set",
"detail": "Measurement set [IGVFDS1327XCCU](/measurement-sets/IGVFDS1327XCCU/) 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/IGVFDS1327XCCU/"
}
]
},
"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": "2023-11-30T22:50:02.992206+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/IGVFFI3781UEFZ/",
"accession": "IGVFFI3781UEFZ",
"aliases": [
"jesse-engreitz:230807S022-THP1-P153-Amp_PPIF_promoter-BioRep2-FFrep3-BinA-PCRrep7_R2"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2023-12-05T22:35:31.292782+00:00",
"file_format": "fastq",
"file_size": 6157683,
"href": "/sequence-files/IGVFFI3781UEFZ/@@download/IGVFFI3781UEFZ.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-BioRep2-FFrep3-BinA-PCRrep7_S295_R2_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI1078IQWD/",
"accession": "IGVFFI1078IQWD",
"aliases": [
"jesse-engreitz:230807S022-THP1-P153-Amp_PPIF_promoter-BioRep2-FFrep3-BinA-PCRrep9_R1"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2023-12-05T22:36:32.741389+00:00",
"file_format": "fastq",
"file_size": 4838886,
"href": "/sequence-files/IGVFFI1078IQWD/@@download/IGVFFI1078IQWD.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-BioRep2-FFrep3-BinA-PCRrep9_S297_R1_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI0174HPHA/",
"accession": "IGVFFI0174HPHA",
"aliases": [
"jesse-engreitz:230807S022-THP1-P153-Amp_PPIF_promoter-BioRep2-FFrep3-BinA-PCRrep10_R1"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2023-12-05T22:30:42.405197+00:00",
"file_format": "fastq",
"file_size": 5078515,
"href": "/sequence-files/IGVFFI0174HPHA/@@download/IGVFFI0174HPHA.fastq.gz",
"s3_uri": "s3://igvf-files/2023/12/05/3c9ec4ad-c133-4612-b5da-44d912d2ef59/IGVFFI0174HPHA.fastq.gz",
"sequencing_platform": {
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"status": "released",
"term_name": "Illumina NextSeq 550"
},
"status": "released",
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"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI4807AAZI/",
"accession": "IGVFFI4807AAZI",
"aliases": [
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],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2023-12-05T22:31:52.951304+00:00",
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"file_size": 4945124,
"href": "/sequence-files/IGVFFI4807AAZI/@@download/IGVFFI4807AAZI.fastq.gz",
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},
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"upload_status": "validated"
},
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"@id": "/sequence-files/IGVFFI6312OYBZ/",
"accession": "IGVFFI6312OYBZ",
"aliases": [
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],
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"controlled_access": false,
"creation_timestamp": "2023-12-05T22:32:01.765857+00:00",
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"status": "released",
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"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI2554OOEP/",
"accession": "IGVFFI2554OOEP",
"aliases": [
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],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2023-12-05T22:30:33.601258+00:00",
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"file_size": 1418062,
"href": "/sequence-files/IGVFFI2554OOEP/@@download/IGVFFI2554OOEP.fastq.gz",
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"status": "released",
"term_name": "Illumina NextSeq 550"
},
"status": "released",
"submitted_file_name": "230807S022-THP1-P153-Amp_PPIF_promoter-BioRep2-FFrep3-BinA-PCRrep10_S298_I2_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI2217TFSA/",
"accession": "IGVFFI2217TFSA",
"aliases": [
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],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2023-12-05T22:34:21.470287+00:00",
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"href": "/sequence-files/IGVFFI2217TFSA/@@download/IGVFFI2217TFSA.fastq.gz",
"s3_uri": "s3://igvf-files/2023/12/05/00fa9434-3a76-42d0-b733-84827b0c2e69/IGVFFI2217TFSA.fastq.gz",
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},
"status": "released",
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"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI8870KVMB/",
"accession": "IGVFFI8870KVMB",
"aliases": [
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],
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},
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"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI6612TAEI/",
"accession": "IGVFFI6612TAEI",
"aliases": [
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],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2023-12-05T22:30:24.852633+00:00",
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"href": "/sequence-files/IGVFFI6612TAEI/@@download/IGVFFI6612TAEI.fastq.gz",
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},
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"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI5180CXKH/",
"accession": "IGVFFI5180CXKH",
"aliases": [
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],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2023-12-05T22:35:48.888870+00:00",
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"status": "released",
"term_name": "Illumina NextSeq 550"
},
"status": "released",
"submitted_file_name": "230807S022-THP1-P153-Amp_PPIF_promoter-BioRep2-FFrep3-BinA-PCRrep8_S296_I2_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI0555LQIR/",
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"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": "e9fc1daf-59f0-47b4-bf37-4cb520190d19"
}