{
"@context": "/terms/",
"@id": "/measurement-sets/IGVFDS5699JBLV/",
"@type": [
"MeasurementSet",
"FileSet",
"Item"
],
"accession": "IGVFDS5699JBLV",
"aliases": [
"jesse-engreitz:230807S022-THP1-P153-Amp_PPIF_promoter-BioRep2-FFrep4-BinC_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 [IGVFDS5699JBLV](/measurement-sets/IGVFDS5699JBLV/) 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/IGVFDS5699JBLV/"
},
{
"category": "missing sequencing kit",
"detail": "Measurement set [IGVFDS5699JBLV](/measurement-sets/IGVFDS5699JBLV/) has sequence file(s) [IGVFFI0958OCGP](/sequence-files/IGVFFI0958OCGP/), [IGVFFI2733FCGF](/sequence-files/IGVFFI2733FCGF/), [IGVFFI8622NJXI](/sequence-files/IGVFFI8622NJXI/), [IGVFFI3151RBXM](/sequence-files/IGVFFI3151RBXM/), [IGVFFI6733QYTJ](/sequence-files/IGVFFI6733QYTJ/), [IGVFFI8454ZFEK](/sequence-files/IGVFFI8454ZFEK/), [IGVFFI6740JDUZ](/sequence-files/IGVFFI6740JDUZ/), [IGVFFI8077WXAY](/sequence-files/IGVFFI8077WXAY/), [IGVFFI5031OMIY](/sequence-files/IGVFFI5031OMIY/), [IGVFFI7217MGWG](/sequence-files/IGVFFI7217MGWG/), [IGVFFI3314MDQA](/sequence-files/IGVFFI3314MDQA/), [IGVFFI1803RIUO](/sequence-files/IGVFFI1803RIUO/), [IGVFFI0679KMFP](/sequence-files/IGVFFI0679KMFP/), [IGVFFI7059RFHS](/sequence-files/IGVFFI7059RFHS/), [IGVFFI9525HCBY](/sequence-files/IGVFFI9525HCBY/), [IGVFFI3799VBPL](/sequence-files/IGVFFI3799VBPL/), [IGVFFI6995QNIF](/sequence-files/IGVFFI6995QNIF/), [IGVFFI8194VCNM](/sequence-files/IGVFFI8194VCNM/), [IGVFFI2700MMKU](/sequence-files/IGVFFI2700MMKU/), [IGVFFI4894RVJK](/sequence-files/IGVFFI4894RVJK/), [IGVFFI7956SGCK](/sequence-files/IGVFFI7956SGCK/), [IGVFFI5994PETN](/sequence-files/IGVFFI5994PETN/), [IGVFFI2920YYJS](/sequence-files/IGVFFI2920YYJS/), [IGVFFI4444PJZQ](/sequence-files/IGVFFI4444PJZQ/), [IGVFFI3467VZAJ](/sequence-files/IGVFFI3467VZAJ/), [IGVFFI0080MGCB](/sequence-files/IGVFFI0080MGCB/), [IGVFFI4705GOIB](/sequence-files/IGVFFI4705GOIB/), [IGVFFI9212LNJI](/sequence-files/IGVFFI9212LNJI/), [IGVFFI9404WKLX](/sequence-files/IGVFFI9404WKLX/), [IGVFFI0543UIGI](/sequence-files/IGVFFI0543UIGI/), [IGVFFI5299QRPK](/sequence-files/IGVFFI5299QRPK/), [IGVFFI2392XLES](/sequence-files/IGVFFI2392XLES/), [IGVFFI7929CUIC](/sequence-files/IGVFFI7929CUIC/), [IGVFFI0928YSSZ](/sequence-files/IGVFFI0928YSSZ/), [IGVFFI9060QDZA](/sequence-files/IGVFFI9060QDZA/), [IGVFFI6422DFEZ](/sequence-files/IGVFFI6422DFEZ/), [IGVFFI8335IMVS](/sequence-files/IGVFFI8335IMVS/), [IGVFFI8726PZBB](/sequence-files/IGVFFI8726PZBB/), [IGVFFI4146PFWX](/sequence-files/IGVFFI4146PFWX/), [IGVFFI2369NAXZ](/sequence-files/IGVFFI2369NAXZ/), [IGVFFI4153TTDF](/sequence-files/IGVFFI4153TTDF/), [IGVFFI4306NZHI](/sequence-files/IGVFFI4306NZHI/), [IGVFFI4108VBGQ](/sequence-files/IGVFFI4108VBGQ/), [IGVFFI7389NPMT](/sequence-files/IGVFFI7389NPMT/), [IGVFFI1992MEDA](/sequence-files/IGVFFI1992MEDA/), [IGVFFI9788GMPZ](/sequence-files/IGVFFI9788GMPZ/), [IGVFFI6078MXLL](/sequence-files/IGVFFI6078MXLL/), [IGVFFI6058ZKOZ](/sequence-files/IGVFFI6058ZKOZ/) 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/IGVFDS5699JBLV/"
},
{
"category": "missing sequence specification",
"detail": "Measurement set [IGVFDS5699JBLV](/measurement-sets/IGVFDS5699JBLV/) has sequence file(s): [IGVFFI0958OCGP](/sequence-files/IGVFFI0958OCGP/), [IGVFFI2733FCGF](/sequence-files/IGVFFI2733FCGF/), [IGVFFI8622NJXI](/sequence-files/IGVFFI8622NJXI/), [IGVFFI3151RBXM](/sequence-files/IGVFFI3151RBXM/), [IGVFFI6733QYTJ](/sequence-files/IGVFFI6733QYTJ/), [IGVFFI8454ZFEK](/sequence-files/IGVFFI8454ZFEK/), [IGVFFI6740JDUZ](/sequence-files/IGVFFI6740JDUZ/), [IGVFFI8077WXAY](/sequence-files/IGVFFI8077WXAY/), [IGVFFI5031OMIY](/sequence-files/IGVFFI5031OMIY/), [IGVFFI7217MGWG](/sequence-files/IGVFFI7217MGWG/), [IGVFFI3314MDQA](/sequence-files/IGVFFI3314MDQA/), [IGVFFI1803RIUO](/sequence-files/IGVFFI1803RIUO/), [IGVFFI0679KMFP](/sequence-files/IGVFFI0679KMFP/), [IGVFFI7059RFHS](/sequence-files/IGVFFI7059RFHS/), [IGVFFI9525HCBY](/sequence-files/IGVFFI9525HCBY/), [IGVFFI3799VBPL](/sequence-files/IGVFFI3799VBPL/), [IGVFFI6995QNIF](/sequence-files/IGVFFI6995QNIF/), [IGVFFI8194VCNM](/sequence-files/IGVFFI8194VCNM/), [IGVFFI2700MMKU](/sequence-files/IGVFFI2700MMKU/), [IGVFFI4894RVJK](/sequence-files/IGVFFI4894RVJK/), [IGVFFI7956SGCK](/sequence-files/IGVFFI7956SGCK/), [IGVFFI5994PETN](/sequence-files/IGVFFI5994PETN/), [IGVFFI2920YYJS](/sequence-files/IGVFFI2920YYJS/), [IGVFFI4444PJZQ](/sequence-files/IGVFFI4444PJZQ/), [IGVFFI3467VZAJ](/sequence-files/IGVFFI3467VZAJ/), [IGVFFI0080MGCB](/sequence-files/IGVFFI0080MGCB/), [IGVFFI4705GOIB](/sequence-files/IGVFFI4705GOIB/), [IGVFFI9212LNJI](/sequence-files/IGVFFI9212LNJI/), [IGVFFI9404WKLX](/sequence-files/IGVFFI9404WKLX/), [IGVFFI0543UIGI](/sequence-files/IGVFFI0543UIGI/), [IGVFFI5299QRPK](/sequence-files/IGVFFI5299QRPK/), [IGVFFI2392XLES](/sequence-files/IGVFFI2392XLES/), [IGVFFI7929CUIC](/sequence-files/IGVFFI7929CUIC/), [IGVFFI0928YSSZ](/sequence-files/IGVFFI0928YSSZ/), [IGVFFI9060QDZA](/sequence-files/IGVFFI9060QDZA/), [IGVFFI6422DFEZ](/sequence-files/IGVFFI6422DFEZ/), [IGVFFI8335IMVS](/sequence-files/IGVFFI8335IMVS/), [IGVFFI8726PZBB](/sequence-files/IGVFFI8726PZBB/), [IGVFFI4146PFWX](/sequence-files/IGVFFI4146PFWX/), [IGVFFI2369NAXZ](/sequence-files/IGVFFI2369NAXZ/), [IGVFFI4153TTDF](/sequence-files/IGVFFI4153TTDF/), [IGVFFI4306NZHI](/sequence-files/IGVFFI4306NZHI/), [IGVFFI4108VBGQ](/sequence-files/IGVFFI4108VBGQ/), [IGVFFI7389NPMT](/sequence-files/IGVFFI7389NPMT/), [IGVFFI1992MEDA](/sequence-files/IGVFFI1992MEDA/), [IGVFFI9788GMPZ](/sequence-files/IGVFFI9788GMPZ/), [IGVFFI6078MXLL](/sequence-files/IGVFFI6078MXLL/), [IGVFFI6058ZKOZ](/sequence-files/IGVFFI6058ZKOZ/) 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/IGVFDS5699JBLV/"
},
{
"category": "mismatched status",
"detail": "Released in vitro system [IGVFSM4853BCZC](/in-vitro-systems/IGVFSM4853BCZC/) 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/IGVFSM4853BCZC/"
},
{
"category": "missing publication",
"detail": "In vitro system [IGVFSM4853BCZC](/in-vitro-systems/IGVFSM4853BCZC/) 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/IGVFSM4853BCZC/"
}
],
"WARNING": [
{
"category": "missing auxiliary set",
"detail": "Measurement set [IGVFDS5699JBLV](/measurement-sets/IGVFDS5699JBLV/) 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/IGVFDS5699JBLV/"
}
]
},
"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": "2023-11-30T22:50:11.952828+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/IGVFFI0958OCGP/",
"accession": "IGVFFI0958OCGP",
"aliases": [
"jesse-engreitz:230807S022-THP1-P153-Amp_PPIF_promoter-BioRep2-FFrep4-BinC-PCRrep3_I1"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2023-12-05T23:14:37.648177+00:00",
"file_format": "fastq",
"file_size": 1463554,
"href": "/sequence-files/IGVFFI0958OCGP/@@download/IGVFFI0958OCGP.fastq.gz",
"s3_uri": "s3://igvf-files/2023/12/05/2ae94c2e-ceb5-4b42-8699-eeea9ec0e0f7/IGVFFI0958OCGP.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-BioRep2-FFrep4-BinC-PCRrep3_S363_I1_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI2733FCGF/",
"accession": "IGVFFI2733FCGF",
"aliases": [
"jesse-engreitz:230807S022-THP1-P153-Amp_PPIF_promoter-BioRep2-FFrep4-BinC-PCRrep3_I2"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2023-12-05T23:14:46.507762+00:00",
"file_format": "fastq",
"file_size": 1398340,
"href": "/sequence-files/IGVFFI2733FCGF/@@download/IGVFFI2733FCGF.fastq.gz",
"s3_uri": "s3://igvf-files/2023/12/05/732440c4-9cc6-4bc8-8b44-8fb76f660844/IGVFFI2733FCGF.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-BinC-PCRrep3_S363_I2_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI8622NJXI/",
"accession": "IGVFFI8622NJXI",
"aliases": [
"jesse-engreitz:230807S022-THP1-P153-Amp_PPIF_promoter-BioRep2-FFrep4-BinC-PCRrep8_I2"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2023-12-05T23:17:41.483321+00:00",
"file_format": "fastq",
"file_size": 1433473,
"href": "/sequence-files/IGVFFI8622NJXI/@@download/IGVFFI8622NJXI.fastq.gz",
"s3_uri": "s3://igvf-files/2023/12/05/65525f37-d0a0-45da-90c0-3a677ce2dc1a/IGVFFI8622NJXI.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-BinC-PCRrep8_S368_I2_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI3151RBXM/",
"accession": "IGVFFI3151RBXM",
"aliases": [
"jesse-engreitz:230807S022-THP1-P153-Amp_PPIF_promoter-BioRep2-FFrep4-BinC-PCRrep5_R2"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2023-12-05T23:16:13.538573+00:00",
"file_format": "fastq",
"file_size": 6410303,
"href": "/sequence-files/IGVFFI3151RBXM/@@download/IGVFFI3151RBXM.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-BinC-PCRrep5_S365_R2_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI6733QYTJ/",
"accession": "IGVFFI6733QYTJ",
"aliases": [
"jesse-engreitz:230807S022-THP1-P153-Amp_PPIF_promoter-BioRep2-FFrep4-BinC-PCRrep4_R2"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2023-12-05T23:15:38.732094+00:00",
"file_format": "fastq",
"file_size": 6428330,
"href": "/sequence-files/IGVFFI6733QYTJ/@@download/IGVFFI6733QYTJ.fastq.gz",
"s3_uri": "s3://igvf-files/2023/12/05/5aa23fff-6b0b-41b9-94c5-d1af6a38ff6c/IGVFFI6733QYTJ.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-BinC-PCRrep4_S364_R2_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI8454ZFEK/",
"accession": "IGVFFI8454ZFEK",
"aliases": [
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],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2023-12-05T23:14:11.504635+00:00",
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"file_size": 1454481,
"href": "/sequence-files/IGVFFI8454ZFEK/@@download/IGVFFI8454ZFEK.fastq.gz",
"s3_uri": "s3://igvf-files/2023/12/05/b5b24be7-05e6-4d58-89ad-04679d810768/IGVFFI8454ZFEK.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-BinC-PCRrep2_S362_I2_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI6740JDUZ/",
"accession": "IGVFFI6740JDUZ",
"aliases": [
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],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2023-12-05T23:12:01.516394+00:00",
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"href": "/sequence-files/IGVFFI6740JDUZ/@@download/IGVFFI6740JDUZ.fastq.gz",
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"term_name": "Illumina NextSeq 550"
},
"status": "released",
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"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI8077WXAY/",
"accession": "IGVFFI8077WXAY",
"aliases": [
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],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2023-12-05T23:17:14.845217+00:00",
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"file_size": 5255478,
"href": "/sequence-files/IGVFFI8077WXAY/@@download/IGVFFI8077WXAY.fastq.gz",
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"term_name": "Illumina NextSeq 550"
},
"status": "released",
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"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI5031OMIY/",
"accession": "IGVFFI5031OMIY",
"aliases": [
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],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2023-12-05T23:12:35.536040+00:00",
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"href": "/sequence-files/IGVFFI5031OMIY/@@download/IGVFFI5031OMIY.fastq.gz",
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"term_name": "Illumina NextSeq 550"
},
"status": "released",
"submitted_file_name": "230807S022-THP1-P153-Amp_PPIF_promoter-BioRep2-FFrep4-BinC-PCRrep10_S370_R1_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI7217MGWG/",
"accession": "IGVFFI7217MGWG",
"aliases": [
"jesse-engreitz:230807S022-THP1-P153-Amp_PPIF_promoter-BioRep2-FFrep4-BinC-PCRrep6_I1"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2023-12-05T23:16:22.407874+00:00",
"file_format": "fastq",
"file_size": 1557563,
"href": "/sequence-files/IGVFFI7217MGWG/@@download/IGVFFI7217MGWG.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-BinC-PCRrep6_S366_I1_001.fastq.gz",
"upload_status": "validated"
},
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"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": "ccdaef89-94d9-4c10-b7cb-1153308374ae"
}