{
"@context": "/terms/",
"@id": "/measurement-sets/IGVFDS1783OBDQ/",
"@type": [
"MeasurementSet",
"FileSet",
"Item"
],
"accession": "IGVFDS1783OBDQ",
"aliases": [
"jesse-engreitz:230807S022-THP1-P153-Amp_PPIF_promoter-BioRep2-FFrep3-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 [IGVFDS1783OBDQ](/measurement-sets/IGVFDS1783OBDQ/) 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/IGVFDS1783OBDQ/"
},
{
"category": "missing sequencing kit",
"detail": "Measurement set [IGVFDS1783OBDQ](/measurement-sets/IGVFDS1783OBDQ/) has sequence file(s) [IGVFFI5273XXMZ](/sequence-files/IGVFFI5273XXMZ/), [IGVFFI1392DWWT](/sequence-files/IGVFFI1392DWWT/), [IGVFFI5454APPU](/sequence-files/IGVFFI5454APPU/), [IGVFFI8365JVYQ](/sequence-files/IGVFFI8365JVYQ/), [IGVFFI5384OHPY](/sequence-files/IGVFFI5384OHPY/), [IGVFFI3445JMTA](/sequence-files/IGVFFI3445JMTA/), [IGVFFI3196UNZG](/sequence-files/IGVFFI3196UNZG/), [IGVFFI3640VZZP](/sequence-files/IGVFFI3640VZZP/), [IGVFFI5966HRBE](/sequence-files/IGVFFI5966HRBE/), [IGVFFI7780BWMD](/sequence-files/IGVFFI7780BWMD/), [IGVFFI1292KVQH](/sequence-files/IGVFFI1292KVQH/), [IGVFFI4963FEUF](/sequence-files/IGVFFI4963FEUF/), [IGVFFI9697VTJX](/sequence-files/IGVFFI9697VTJX/), [IGVFFI3918IXHP](/sequence-files/IGVFFI3918IXHP/), [IGVFFI1419EGJU](/sequence-files/IGVFFI1419EGJU/), [IGVFFI7553WZJO](/sequence-files/IGVFFI7553WZJO/), [IGVFFI3401PMYQ](/sequence-files/IGVFFI3401PMYQ/), [IGVFFI4328ILVD](/sequence-files/IGVFFI4328ILVD/), [IGVFFI9981FXPK](/sequence-files/IGVFFI9981FXPK/), [IGVFFI2821MKFB](/sequence-files/IGVFFI2821MKFB/), [IGVFFI2164MEMX](/sequence-files/IGVFFI2164MEMX/), [IGVFFI2372UNMC](/sequence-files/IGVFFI2372UNMC/), [IGVFFI4490WQLD](/sequence-files/IGVFFI4490WQLD/), [IGVFFI3894JBGH](/sequence-files/IGVFFI3894JBGH/), [IGVFFI5865IQFR](/sequence-files/IGVFFI5865IQFR/), [IGVFFI6644FHZZ](/sequence-files/IGVFFI6644FHZZ/), [IGVFFI2787RXXU](/sequence-files/IGVFFI2787RXXU/), [IGVFFI6070NNFA](/sequence-files/IGVFFI6070NNFA/), [IGVFFI1468BKHX](/sequence-files/IGVFFI1468BKHX/), [IGVFFI4906AQJD](/sequence-files/IGVFFI4906AQJD/), [IGVFFI4323LSBH](/sequence-files/IGVFFI4323LSBH/), [IGVFFI2292PYPW](/sequence-files/IGVFFI2292PYPW/), [IGVFFI8098YOGQ](/sequence-files/IGVFFI8098YOGQ/), [IGVFFI8834HKHY](/sequence-files/IGVFFI8834HKHY/), [IGVFFI0700KBYN](/sequence-files/IGVFFI0700KBYN/), [IGVFFI8234BGBN](/sequence-files/IGVFFI8234BGBN/), [IGVFFI8394CAAJ](/sequence-files/IGVFFI8394CAAJ/), [IGVFFI9489NFMA](/sequence-files/IGVFFI9489NFMA/), [IGVFFI5634QVAU](/sequence-files/IGVFFI5634QVAU/), [IGVFFI1084WWWI](/sequence-files/IGVFFI1084WWWI/), [IGVFFI1587HKAU](/sequence-files/IGVFFI1587HKAU/), [IGVFFI7868ERJC](/sequence-files/IGVFFI7868ERJC/), [IGVFFI4266WRZV](/sequence-files/IGVFFI4266WRZV/), [IGVFFI6570GECU](/sequence-files/IGVFFI6570GECU/), [IGVFFI1544GAUM](/sequence-files/IGVFFI1544GAUM/), [IGVFFI9353KKSR](/sequence-files/IGVFFI9353KKSR/), [IGVFFI8157LOFU](/sequence-files/IGVFFI8157LOFU/), [IGVFFI6256RSXK](/sequence-files/IGVFFI6256RSXK/) 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/IGVFDS1783OBDQ/"
},
{
"category": "missing sequence specification",
"detail": "Measurement set [IGVFDS1783OBDQ](/measurement-sets/IGVFDS1783OBDQ/) has sequence file(s): [IGVFFI5273XXMZ](/sequence-files/IGVFFI5273XXMZ/), [IGVFFI1392DWWT](/sequence-files/IGVFFI1392DWWT/), [IGVFFI5454APPU](/sequence-files/IGVFFI5454APPU/), [IGVFFI8365JVYQ](/sequence-files/IGVFFI8365JVYQ/), [IGVFFI5384OHPY](/sequence-files/IGVFFI5384OHPY/), [IGVFFI3445JMTA](/sequence-files/IGVFFI3445JMTA/), [IGVFFI3196UNZG](/sequence-files/IGVFFI3196UNZG/), [IGVFFI3640VZZP](/sequence-files/IGVFFI3640VZZP/), [IGVFFI5966HRBE](/sequence-files/IGVFFI5966HRBE/), [IGVFFI7780BWMD](/sequence-files/IGVFFI7780BWMD/), [IGVFFI1292KVQH](/sequence-files/IGVFFI1292KVQH/), [IGVFFI4963FEUF](/sequence-files/IGVFFI4963FEUF/), [IGVFFI9697VTJX](/sequence-files/IGVFFI9697VTJX/), [IGVFFI3918IXHP](/sequence-files/IGVFFI3918IXHP/), [IGVFFI1419EGJU](/sequence-files/IGVFFI1419EGJU/), [IGVFFI7553WZJO](/sequence-files/IGVFFI7553WZJO/), [IGVFFI3401PMYQ](/sequence-files/IGVFFI3401PMYQ/), [IGVFFI4328ILVD](/sequence-files/IGVFFI4328ILVD/), [IGVFFI9981FXPK](/sequence-files/IGVFFI9981FXPK/), [IGVFFI2821MKFB](/sequence-files/IGVFFI2821MKFB/), [IGVFFI2164MEMX](/sequence-files/IGVFFI2164MEMX/), [IGVFFI2372UNMC](/sequence-files/IGVFFI2372UNMC/), [IGVFFI4490WQLD](/sequence-files/IGVFFI4490WQLD/), [IGVFFI3894JBGH](/sequence-files/IGVFFI3894JBGH/), [IGVFFI5865IQFR](/sequence-files/IGVFFI5865IQFR/), [IGVFFI6644FHZZ](/sequence-files/IGVFFI6644FHZZ/), [IGVFFI2787RXXU](/sequence-files/IGVFFI2787RXXU/), [IGVFFI6070NNFA](/sequence-files/IGVFFI6070NNFA/), [IGVFFI1468BKHX](/sequence-files/IGVFFI1468BKHX/), [IGVFFI4906AQJD](/sequence-files/IGVFFI4906AQJD/), [IGVFFI4323LSBH](/sequence-files/IGVFFI4323LSBH/), [IGVFFI2292PYPW](/sequence-files/IGVFFI2292PYPW/), [IGVFFI8098YOGQ](/sequence-files/IGVFFI8098YOGQ/), [IGVFFI8834HKHY](/sequence-files/IGVFFI8834HKHY/), [IGVFFI0700KBYN](/sequence-files/IGVFFI0700KBYN/), [IGVFFI8234BGBN](/sequence-files/IGVFFI8234BGBN/), [IGVFFI8394CAAJ](/sequence-files/IGVFFI8394CAAJ/), [IGVFFI9489NFMA](/sequence-files/IGVFFI9489NFMA/), [IGVFFI5634QVAU](/sequence-files/IGVFFI5634QVAU/), [IGVFFI1084WWWI](/sequence-files/IGVFFI1084WWWI/), [IGVFFI1587HKAU](/sequence-files/IGVFFI1587HKAU/), [IGVFFI7868ERJC](/sequence-files/IGVFFI7868ERJC/), [IGVFFI4266WRZV](/sequence-files/IGVFFI4266WRZV/), [IGVFFI6570GECU](/sequence-files/IGVFFI6570GECU/), [IGVFFI1544GAUM](/sequence-files/IGVFFI1544GAUM/), [IGVFFI9353KKSR](/sequence-files/IGVFFI9353KKSR/), [IGVFFI8157LOFU](/sequence-files/IGVFFI8157LOFU/), [IGVFFI6256RSXK](/sequence-files/IGVFFI6256RSXK/) 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/IGVFDS1783OBDQ/"
},
{
"category": "mismatched status",
"detail": "Released in vitro system [IGVFSM3986RDKP](/in-vitro-systems/IGVFSM3986RDKP/) 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/IGVFSM3986RDKP/"
},
{
"category": "missing publication",
"detail": "In vitro system [IGVFSM3986RDKP](/in-vitro-systems/IGVFSM3986RDKP/) 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/IGVFSM3986RDKP/"
}
],
"WARNING": [
{
"category": "missing auxiliary set",
"detail": "Measurement set [IGVFDS1783OBDQ](/measurement-sets/IGVFDS1783OBDQ/) 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/IGVFDS1783OBDQ/"
}
]
},
"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": "2023-11-30T22:50:05.260621+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/IGVFFI5273XXMZ/",
"accession": "IGVFFI5273XXMZ",
"aliases": [
"jesse-engreitz:230807S022-THP1-P153-Amp_PPIF_promoter-BioRep2-FFrep3-BinB-PCRrep4_I2"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2023-12-05T22:40:28.531440+00:00",
"file_format": "fastq",
"file_size": 1450809,
"href": "/sequence-files/IGVFFI5273XXMZ/@@download/IGVFFI5273XXMZ.fastq.gz",
"s3_uri": "s3://igvf-files/2023/12/05/4088645e-549a-4799-8333-662e91685556/IGVFFI5273XXMZ.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-FFrep3-BinB-PCRrep4_S304_I2_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI1392DWWT/",
"accession": "IGVFFI1392DWWT",
"aliases": [
"jesse-engreitz:230807S022-THP1-P153-Amp_PPIF_promoter-BioRep2-FFrep3-BinB-PCRrep1_R2"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2023-12-05T22:37:16.547734+00:00",
"file_format": "fastq",
"file_size": 6312793,
"href": "/sequence-files/IGVFFI1392DWWT/@@download/IGVFFI1392DWWT.fastq.gz",
"s3_uri": "s3://igvf-files/2023/12/05/90fe6be1-c230-4cbf-8f0d-07ac0c4c3820/IGVFFI1392DWWT.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-FFrep3-BinB-PCRrep1_S301_R2_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI5454APPU/",
"accession": "IGVFFI5454APPU",
"aliases": [
"jesse-engreitz:230807S022-THP1-P153-Amp_PPIF_promoter-BioRep2-FFrep3-BinB-PCRrep5_R1"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2023-12-05T22:41:12.244893+00:00",
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"file_size": 4931936,
"href": "/sequence-files/IGVFFI5454APPU/@@download/IGVFFI5454APPU.fastq.gz",
"s3_uri": "s3://igvf-files/2023/12/05/7c23a046-7673-4334-bf36-c19b07b0b824/IGVFFI5454APPU.fastq.gz",
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"status": "released",
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},
"status": "released",
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"upload_status": "validated"
},
{
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],
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"creation_timestamp": "2023-12-05T22:41:38.372173+00:00",
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"href": "/sequence-files/IGVFFI8365JVYQ/@@download/IGVFFI8365JVYQ.fastq.gz",
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},
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"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI5384OHPY/",
"accession": "IGVFFI5384OHPY",
"aliases": [
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],
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"controlled_access": false,
"creation_timestamp": "2023-12-05T22:42:31.029125+00:00",
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"href": "/sequence-files/IGVFFI5384OHPY/@@download/IGVFFI5384OHPY.fastq.gz",
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"status": "released",
"term_name": "Illumina NextSeq 550"
},
"status": "released",
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"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI3445JMTA/",
"accession": "IGVFFI3445JMTA",
"aliases": [
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],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2023-12-05T22:43:32.107418+00:00",
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"file_size": 4895763,
"href": "/sequence-files/IGVFFI3445JMTA/@@download/IGVFFI3445JMTA.fastq.gz",
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},
"status": "released",
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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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],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2023-12-05T22:42:22.318820+00:00",
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},
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"upload_status": "validated"
},
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"accession": "IGVFFI5966HRBE",
"aliases": [
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],
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"controlled_access": false,
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},
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"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI7780BWMD/",
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"aliases": [
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],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2023-12-05T22:42:48.486203+00:00",
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},
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"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI1292KVQH/",
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"CyP-M",
"cyclophilin F",
"peptidyl-prolyl cis-trans isomerase, mitochondrial",
"cyclophilin 3",
"cyclophilin D",
"rotamase F",
"mitochondrial cyclophilin",
"CypD",
"CYP3"
]
}
],
"uuid": "306ad3e9-1974-44cb-9f19-f9aeb3702478"
}