{
"@context": "/terms/",
"@id": "/measurement-sets/IGVFDS4715UUNW/",
"@type": [
"MeasurementSet",
"FileSet",
"Item"
],
"accession": "IGVFDS4715UUNW",
"aliases": [
"jesse-engreitz:230807S022-THP1-P153-Amp_PPIF_promoter-BioRep2-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": "mismatched status",
"detail": "Released in vitro system [IGVFSM6465SGTZ](/in-vitro-systems/IGVFSM6465SGTZ/) 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/IGVFSM6465SGTZ/"
},
{
"category": "missing publication",
"detail": "In vitro system [IGVFSM6465SGTZ](/in-vitro-systems/IGVFSM6465SGTZ/) 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/IGVFSM6465SGTZ/"
},
{
"category": "missing publication",
"detail": "Measurement set [IGVFDS4715UUNW](/measurement-sets/IGVFDS4715UUNW/) 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/IGVFDS4715UUNW/"
},
{
"category": "missing sequencing kit",
"detail": "Measurement set [IGVFDS4715UUNW](/measurement-sets/IGVFDS4715UUNW/) has sequence file(s) [IGVFFI3607YKUC](/sequence-files/IGVFFI3607YKUC/), [IGVFFI6218NFQS](/sequence-files/IGVFFI6218NFQS/), [IGVFFI0274PUXE](/sequence-files/IGVFFI0274PUXE/), [IGVFFI5125IDOE](/sequence-files/IGVFFI5125IDOE/), [IGVFFI4610QDGV](/sequence-files/IGVFFI4610QDGV/), [IGVFFI4594INBA](/sequence-files/IGVFFI4594INBA/), [IGVFFI6251VYGU](/sequence-files/IGVFFI6251VYGU/), [IGVFFI3994GSTL](/sequence-files/IGVFFI3994GSTL/), [IGVFFI1944OUXD](/sequence-files/IGVFFI1944OUXD/), [IGVFFI9184CZBD](/sequence-files/IGVFFI9184CZBD/), [IGVFFI9772SKUX](/sequence-files/IGVFFI9772SKUX/), [IGVFFI8929XKOB](/sequence-files/IGVFFI8929XKOB/), [IGVFFI1499WAPM](/sequence-files/IGVFFI1499WAPM/), [IGVFFI6377VEIZ](/sequence-files/IGVFFI6377VEIZ/), [IGVFFI4955KZXD](/sequence-files/IGVFFI4955KZXD/), [IGVFFI9325JLRR](/sequence-files/IGVFFI9325JLRR/), [IGVFFI9229IWPT](/sequence-files/IGVFFI9229IWPT/), [IGVFFI7985PIGO](/sequence-files/IGVFFI7985PIGO/), [IGVFFI2274SCHL](/sequence-files/IGVFFI2274SCHL/), [IGVFFI7410FPKB](/sequence-files/IGVFFI7410FPKB/), [IGVFFI2937NHTG](/sequence-files/IGVFFI2937NHTG/), [IGVFFI0412PDLA](/sequence-files/IGVFFI0412PDLA/), [IGVFFI0823QNJP](/sequence-files/IGVFFI0823QNJP/), [IGVFFI2926TOQM](/sequence-files/IGVFFI2926TOQM/), [IGVFFI7284RNWP](/sequence-files/IGVFFI7284RNWP/), [IGVFFI3110BEYO](/sequence-files/IGVFFI3110BEYO/), [IGVFFI3144HJFC](/sequence-files/IGVFFI3144HJFC/), [IGVFFI9973MEOU](/sequence-files/IGVFFI9973MEOU/), [IGVFFI6880IFRV](/sequence-files/IGVFFI6880IFRV/), [IGVFFI8420JRAJ](/sequence-files/IGVFFI8420JRAJ/), [IGVFFI2327HPPA](/sequence-files/IGVFFI2327HPPA/), [IGVFFI7001JZLG](/sequence-files/IGVFFI7001JZLG/), [IGVFFI5242IPQS](/sequence-files/IGVFFI5242IPQS/), [IGVFFI7552QIXL](/sequence-files/IGVFFI7552QIXL/), [IGVFFI0914AOQT](/sequence-files/IGVFFI0914AOQT/), [IGVFFI4356OTRP](/sequence-files/IGVFFI4356OTRP/), [IGVFFI5784GOVY](/sequence-files/IGVFFI5784GOVY/), [IGVFFI7524IGSV](/sequence-files/IGVFFI7524IGSV/), [IGVFFI5611IJQX](/sequence-files/IGVFFI5611IJQX/), [IGVFFI2250LSBK](/sequence-files/IGVFFI2250LSBK/), [IGVFFI2130ELMO](/sequence-files/IGVFFI2130ELMO/), [IGVFFI4103UDVM](/sequence-files/IGVFFI4103UDVM/), [IGVFFI9536XBVG](/sequence-files/IGVFFI9536XBVG/), [IGVFFI7140GDWU](/sequence-files/IGVFFI7140GDWU/), [IGVFFI2160VMLA](/sequence-files/IGVFFI2160VMLA/), [IGVFFI2689JYVN](/sequence-files/IGVFFI2689JYVN/), [IGVFFI4708VMRK](/sequence-files/IGVFFI4708VMRK/), [IGVFFI8617JKDI](/sequence-files/IGVFFI8617JKDI/) 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/IGVFDS4715UUNW/"
},
{
"category": "missing sequence specification",
"detail": "Measurement set [IGVFDS4715UUNW](/measurement-sets/IGVFDS4715UUNW/) has sequence file(s): [IGVFFI3607YKUC](/sequence-files/IGVFFI3607YKUC/), [IGVFFI6218NFQS](/sequence-files/IGVFFI6218NFQS/), [IGVFFI0274PUXE](/sequence-files/IGVFFI0274PUXE/), [IGVFFI5125IDOE](/sequence-files/IGVFFI5125IDOE/), [IGVFFI4610QDGV](/sequence-files/IGVFFI4610QDGV/), [IGVFFI4594INBA](/sequence-files/IGVFFI4594INBA/), [IGVFFI6251VYGU](/sequence-files/IGVFFI6251VYGU/), [IGVFFI3994GSTL](/sequence-files/IGVFFI3994GSTL/), [IGVFFI1944OUXD](/sequence-files/IGVFFI1944OUXD/), [IGVFFI9184CZBD](/sequence-files/IGVFFI9184CZBD/), [IGVFFI9772SKUX](/sequence-files/IGVFFI9772SKUX/), [IGVFFI8929XKOB](/sequence-files/IGVFFI8929XKOB/), [IGVFFI1499WAPM](/sequence-files/IGVFFI1499WAPM/), [IGVFFI6377VEIZ](/sequence-files/IGVFFI6377VEIZ/), [IGVFFI4955KZXD](/sequence-files/IGVFFI4955KZXD/), [IGVFFI9325JLRR](/sequence-files/IGVFFI9325JLRR/), [IGVFFI9229IWPT](/sequence-files/IGVFFI9229IWPT/), [IGVFFI7985PIGO](/sequence-files/IGVFFI7985PIGO/), [IGVFFI2274SCHL](/sequence-files/IGVFFI2274SCHL/), [IGVFFI7410FPKB](/sequence-files/IGVFFI7410FPKB/), [IGVFFI2937NHTG](/sequence-files/IGVFFI2937NHTG/), [IGVFFI0412PDLA](/sequence-files/IGVFFI0412PDLA/), [IGVFFI0823QNJP](/sequence-files/IGVFFI0823QNJP/), [IGVFFI2926TOQM](/sequence-files/IGVFFI2926TOQM/), [IGVFFI7284RNWP](/sequence-files/IGVFFI7284RNWP/), [IGVFFI3110BEYO](/sequence-files/IGVFFI3110BEYO/), [IGVFFI3144HJFC](/sequence-files/IGVFFI3144HJFC/), [IGVFFI9973MEOU](/sequence-files/IGVFFI9973MEOU/), [IGVFFI6880IFRV](/sequence-files/IGVFFI6880IFRV/), [IGVFFI8420JRAJ](/sequence-files/IGVFFI8420JRAJ/), [IGVFFI2327HPPA](/sequence-files/IGVFFI2327HPPA/), [IGVFFI7001JZLG](/sequence-files/IGVFFI7001JZLG/), [IGVFFI5242IPQS](/sequence-files/IGVFFI5242IPQS/), [IGVFFI7552QIXL](/sequence-files/IGVFFI7552QIXL/), [IGVFFI0914AOQT](/sequence-files/IGVFFI0914AOQT/), [IGVFFI4356OTRP](/sequence-files/IGVFFI4356OTRP/), [IGVFFI5784GOVY](/sequence-files/IGVFFI5784GOVY/), [IGVFFI7524IGSV](/sequence-files/IGVFFI7524IGSV/), [IGVFFI5611IJQX](/sequence-files/IGVFFI5611IJQX/), [IGVFFI2250LSBK](/sequence-files/IGVFFI2250LSBK/), [IGVFFI2130ELMO](/sequence-files/IGVFFI2130ELMO/), [IGVFFI4103UDVM](/sequence-files/IGVFFI4103UDVM/), [IGVFFI9536XBVG](/sequence-files/IGVFFI9536XBVG/), [IGVFFI7140GDWU](/sequence-files/IGVFFI7140GDWU/), [IGVFFI2160VMLA](/sequence-files/IGVFFI2160VMLA/), [IGVFFI2689JYVN](/sequence-files/IGVFFI2689JYVN/), [IGVFFI4708VMRK](/sequence-files/IGVFFI4708VMRK/), [IGVFFI8617JKDI](/sequence-files/IGVFFI8617JKDI/) 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/IGVFDS4715UUNW/"
}
],
"WARNING": [
{
"category": "missing auxiliary set",
"detail": "Measurement set [IGVFDS4715UUNW](/measurement-sets/IGVFDS4715UUNW/) 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/IGVFDS4715UUNW/"
}
]
},
"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": "2023-11-30T22:50:10.832992+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/IGVFFI3607YKUC/",
"accession": "IGVFFI3607YKUC",
"aliases": [
"jesse-engreitz:230807S022-THP1-P153-Amp_PPIF_promoter-BioRep2-FFrep4-BinB-PCRrep11_I1"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2023-12-05T23:05:53.500999+00:00",
"file_format": "fastq",
"file_size": 1460868,
"href": "/sequence-files/IGVFFI3607YKUC/@@download/IGVFFI3607YKUC.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-FFrep4-BinB-PCRrep11_S359_I1_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI6218NFQS/",
"accession": "IGVFFI6218NFQS",
"aliases": [
"jesse-engreitz:230807S022-THP1-P153-Amp_PPIF_promoter-BioRep2-FFrep4-BinB-PCRrep5_I2"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2023-12-05T23:08:57.412621+00:00",
"file_format": "fastq",
"file_size": 1439472,
"href": "/sequence-files/IGVFFI6218NFQS/@@download/IGVFFI6218NFQS.fastq.gz",
"s3_uri": "s3://igvf-files/2023/12/05/467ae122-2237-4465-b0a2-b062b04c3fae/IGVFFI6218NFQS.fastq.gz",
"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-FFrep4-BinB-PCRrep5_S353_I2_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI0274PUXE/",
"accession": "IGVFFI0274PUXE",
"aliases": [
"jesse-engreitz:230807S022-THP1-P153-Amp_PPIF_promoter-BioRep2-FFrep4-BinB-PCRrep2_R2"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2023-12-05T23:07:29.664483+00:00",
"file_format": "fastq",
"file_size": 6007483,
"href": "/sequence-files/IGVFFI0274PUXE/@@download/IGVFFI0274PUXE.fastq.gz",
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},
"status": "released",
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"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI5125IDOE/",
"accession": "IGVFFI5125IDOE",
"aliases": [
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],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2023-12-05T23:11:09.026989+00:00",
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"href": "/sequence-files/IGVFFI5125IDOE/@@download/IGVFFI5125IDOE.fastq.gz",
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"term_name": "Illumina NextSeq 550"
},
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"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI4610QDGV/",
"accession": "IGVFFI4610QDGV",
"aliases": [
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],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2023-12-05T23:10:15.780209+00:00",
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},
"status": "released",
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"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI4594INBA/",
"accession": "IGVFFI4594INBA",
"aliases": [
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],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2023-12-05T23:10:59.397788+00:00",
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"href": "/sequence-files/IGVFFI4594INBA/@@download/IGVFFI4594INBA.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-FFrep4-BinB-PCRrep8_S356_R2_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI6251VYGU/",
"accession": "IGVFFI6251VYGU",
"aliases": [
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],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2023-12-05T23:04:43.469258+00:00",
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"href": "/sequence-files/IGVFFI6251VYGU/@@download/IGVFFI6251VYGU.fastq.gz",
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},
"status": "released",
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"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI3994GSTL/",
"accession": "IGVFFI3994GSTL",
"aliases": [
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],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2023-12-05T23:05:44.700670+00:00",
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},
"status": "released",
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"upload_status": "validated"
},
{
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"accession": "IGVFFI1944OUXD",
"aliases": [
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],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2023-12-05T23:08:30.959900+00:00",
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"href": "/sequence-files/IGVFFI1944OUXD/@@download/IGVFFI1944OUXD.fastq.gz",
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},
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"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI9184CZBD/",
"accession": "IGVFFI9184CZBD",
"aliases": [
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],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2023-12-05T23:07:20.824207+00:00",
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"href": "/sequence-files/IGVFFI9184CZBD/@@download/IGVFFI9184CZBD.fastq.gz",
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"term_name": "Illumina NextSeq 550"
},
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"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI9772SKUX/",
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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": "c347f985-d209-45b2-9862-928f792992b9"
}