{
"@context": "/terms/",
"@id": "/measurement-sets/IGVFDS8517SHZG/",
"@type": [
"MeasurementSet",
"FileSet",
"Item"
],
"accession": "IGVFDS8517SHZG",
"aliases": [
"jesse-engreitz:230807S022-THP1-P153-Amp_PPIF_promoter-BioRep2-FFrep2-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 [IGVFDS8517SHZG](/measurement-sets/IGVFDS8517SHZG/) 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/IGVFDS8517SHZG/"
},
{
"category": "missing sequencing kit",
"detail": "Measurement set [IGVFDS8517SHZG](/measurement-sets/IGVFDS8517SHZG/) has sequence file(s) [IGVFFI0786YLTV](/sequence-files/IGVFFI0786YLTV/), [IGVFFI4077AOQG](/sequence-files/IGVFFI4077AOQG/), [IGVFFI2266UYYN](/sequence-files/IGVFFI2266UYYN/), [IGVFFI0800EEXN](/sequence-files/IGVFFI0800EEXN/), [IGVFFI5299LSFY](/sequence-files/IGVFFI5299LSFY/), [IGVFFI9825WHZM](/sequence-files/IGVFFI9825WHZM/), [IGVFFI5190IWYZ](/sequence-files/IGVFFI5190IWYZ/), [IGVFFI1411ARZI](/sequence-files/IGVFFI1411ARZI/), [IGVFFI0767UQNW](/sequence-files/IGVFFI0767UQNW/), [IGVFFI1236IUVB](/sequence-files/IGVFFI1236IUVB/), [IGVFFI4306LMZR](/sequence-files/IGVFFI4306LMZR/), [IGVFFI3064OWJY](/sequence-files/IGVFFI3064OWJY/), [IGVFFI1617WSPF](/sequence-files/IGVFFI1617WSPF/), [IGVFFI9845WTKK](/sequence-files/IGVFFI9845WTKK/), [IGVFFI6994LGFG](/sequence-files/IGVFFI6994LGFG/), [IGVFFI9531ETAI](/sequence-files/IGVFFI9531ETAI/), [IGVFFI5652NRME](/sequence-files/IGVFFI5652NRME/), [IGVFFI0533BEBH](/sequence-files/IGVFFI0533BEBH/), [IGVFFI1457IZNE](/sequence-files/IGVFFI1457IZNE/), [IGVFFI2591WMRY](/sequence-files/IGVFFI2591WMRY/), [IGVFFI9869AHBS](/sequence-files/IGVFFI9869AHBS/), [IGVFFI0755NBOR](/sequence-files/IGVFFI0755NBOR/), [IGVFFI8132FNYQ](/sequence-files/IGVFFI8132FNYQ/), [IGVFFI4290TUGE](/sequence-files/IGVFFI4290TUGE/), [IGVFFI8614ATCQ](/sequence-files/IGVFFI8614ATCQ/), [IGVFFI6952BIQE](/sequence-files/IGVFFI6952BIQE/), [IGVFFI5799YYQG](/sequence-files/IGVFFI5799YYQG/), [IGVFFI6031NWVD](/sequence-files/IGVFFI6031NWVD/), [IGVFFI0605OUSO](/sequence-files/IGVFFI0605OUSO/), [IGVFFI6819OZVW](/sequence-files/IGVFFI6819OZVW/), [IGVFFI6557BGFE](/sequence-files/IGVFFI6557BGFE/), [IGVFFI4522GLML](/sequence-files/IGVFFI4522GLML/), [IGVFFI5184USTP](/sequence-files/IGVFFI5184USTP/), [IGVFFI5024QCKP](/sequence-files/IGVFFI5024QCKP/), [IGVFFI4930WDWS](/sequence-files/IGVFFI4930WDWS/), [IGVFFI4368IFSI](/sequence-files/IGVFFI4368IFSI/), [IGVFFI8130BHAE](/sequence-files/IGVFFI8130BHAE/), [IGVFFI4399POXT](/sequence-files/IGVFFI4399POXT/), [IGVFFI9788TNVD](/sequence-files/IGVFFI9788TNVD/), [IGVFFI8463GSUS](/sequence-files/IGVFFI8463GSUS/), [IGVFFI2537RBCD](/sequence-files/IGVFFI2537RBCD/), [IGVFFI1655EAEO](/sequence-files/IGVFFI1655EAEO/), [IGVFFI6884FQGD](/sequence-files/IGVFFI6884FQGD/), [IGVFFI8401IBDT](/sequence-files/IGVFFI8401IBDT/), [IGVFFI4892OWDC](/sequence-files/IGVFFI4892OWDC/), [IGVFFI2117VXUO](/sequence-files/IGVFFI2117VXUO/), [IGVFFI8538IGQA](/sequence-files/IGVFFI8538IGQA/), [IGVFFI8614OVLD](/sequence-files/IGVFFI8614OVLD/) 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/IGVFDS8517SHZG/"
},
{
"category": "missing sequence specification",
"detail": "Measurement set [IGVFDS8517SHZG](/measurement-sets/IGVFDS8517SHZG/) has sequence file(s): [IGVFFI0786YLTV](/sequence-files/IGVFFI0786YLTV/), [IGVFFI4077AOQG](/sequence-files/IGVFFI4077AOQG/), [IGVFFI2266UYYN](/sequence-files/IGVFFI2266UYYN/), [IGVFFI0800EEXN](/sequence-files/IGVFFI0800EEXN/), [IGVFFI5299LSFY](/sequence-files/IGVFFI5299LSFY/), [IGVFFI9825WHZM](/sequence-files/IGVFFI9825WHZM/), [IGVFFI5190IWYZ](/sequence-files/IGVFFI5190IWYZ/), [IGVFFI1411ARZI](/sequence-files/IGVFFI1411ARZI/), [IGVFFI0767UQNW](/sequence-files/IGVFFI0767UQNW/), [IGVFFI1236IUVB](/sequence-files/IGVFFI1236IUVB/), [IGVFFI4306LMZR](/sequence-files/IGVFFI4306LMZR/), [IGVFFI3064OWJY](/sequence-files/IGVFFI3064OWJY/), [IGVFFI1617WSPF](/sequence-files/IGVFFI1617WSPF/), [IGVFFI9845WTKK](/sequence-files/IGVFFI9845WTKK/), [IGVFFI6994LGFG](/sequence-files/IGVFFI6994LGFG/), [IGVFFI9531ETAI](/sequence-files/IGVFFI9531ETAI/), [IGVFFI5652NRME](/sequence-files/IGVFFI5652NRME/), [IGVFFI0533BEBH](/sequence-files/IGVFFI0533BEBH/), [IGVFFI1457IZNE](/sequence-files/IGVFFI1457IZNE/), [IGVFFI2591WMRY](/sequence-files/IGVFFI2591WMRY/), [IGVFFI9869AHBS](/sequence-files/IGVFFI9869AHBS/), [IGVFFI0755NBOR](/sequence-files/IGVFFI0755NBOR/), [IGVFFI8132FNYQ](/sequence-files/IGVFFI8132FNYQ/), [IGVFFI4290TUGE](/sequence-files/IGVFFI4290TUGE/), [IGVFFI8614ATCQ](/sequence-files/IGVFFI8614ATCQ/), [IGVFFI6952BIQE](/sequence-files/IGVFFI6952BIQE/), [IGVFFI5799YYQG](/sequence-files/IGVFFI5799YYQG/), [IGVFFI6031NWVD](/sequence-files/IGVFFI6031NWVD/), [IGVFFI0605OUSO](/sequence-files/IGVFFI0605OUSO/), [IGVFFI6819OZVW](/sequence-files/IGVFFI6819OZVW/), [IGVFFI6557BGFE](/sequence-files/IGVFFI6557BGFE/), [IGVFFI4522GLML](/sequence-files/IGVFFI4522GLML/), [IGVFFI5184USTP](/sequence-files/IGVFFI5184USTP/), [IGVFFI5024QCKP](/sequence-files/IGVFFI5024QCKP/), [IGVFFI4930WDWS](/sequence-files/IGVFFI4930WDWS/), [IGVFFI4368IFSI](/sequence-files/IGVFFI4368IFSI/), [IGVFFI8130BHAE](/sequence-files/IGVFFI8130BHAE/), [IGVFFI4399POXT](/sequence-files/IGVFFI4399POXT/), [IGVFFI9788TNVD](/sequence-files/IGVFFI9788TNVD/), [IGVFFI8463GSUS](/sequence-files/IGVFFI8463GSUS/), [IGVFFI2537RBCD](/sequence-files/IGVFFI2537RBCD/), [IGVFFI1655EAEO](/sequence-files/IGVFFI1655EAEO/), [IGVFFI6884FQGD](/sequence-files/IGVFFI6884FQGD/), [IGVFFI8401IBDT](/sequence-files/IGVFFI8401IBDT/), [IGVFFI4892OWDC](/sequence-files/IGVFFI4892OWDC/), [IGVFFI2117VXUO](/sequence-files/IGVFFI2117VXUO/), [IGVFFI8538IGQA](/sequence-files/IGVFFI8538IGQA/), [IGVFFI8614OVLD](/sequence-files/IGVFFI8614OVLD/) 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/IGVFDS8517SHZG/"
},
{
"category": "mismatched status",
"detail": "Released in vitro system [IGVFSM8427KPPU](/in-vitro-systems/IGVFSM8427KPPU/) 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/IGVFSM8427KPPU/"
},
{
"category": "missing publication",
"detail": "In vitro system [IGVFSM8427KPPU](/in-vitro-systems/IGVFSM8427KPPU/) 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/IGVFSM8427KPPU/"
}
],
"WARNING": [
{
"category": "missing auxiliary set",
"detail": "Measurement set [IGVFDS8517SHZG](/measurement-sets/IGVFDS8517SHZG/) 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/IGVFDS8517SHZG/"
}
]
},
"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": "2023-11-30T22:50:00.675615+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/IGVFFI0786YLTV/",
"accession": "IGVFFI0786YLTV",
"aliases": [
"jesse-engreitz:230807S022-THP1-P153-Amp_PPIF_promoter-BioRep2-FFrep2-BinC-PCRrep1_R1"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2023-12-05T22:16:05.220147+00:00",
"file_format": "fastq",
"file_size": 4617427,
"href": "/sequence-files/IGVFFI0786YLTV/@@download/IGVFFI0786YLTV.fastq.gz",
"s3_uri": "s3://igvf-files/2023/12/05/2cd505d0-e896-4c6f-b3eb-d2acae7741ed/IGVFFI0786YLTV.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-FFrep2-BinC-PCRrep1_S265_R1_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI4077AOQG/",
"accession": "IGVFFI4077AOQG",
"aliases": [
"jesse-engreitz:230807S022-THP1-P153-Amp_PPIF_promoter-BioRep2-FFrep2-BinC-PCRrep8_R2"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2023-12-05T22:22:07.860238+00:00",
"file_format": "fastq",
"file_size": 5518784,
"href": "/sequence-files/IGVFFI4077AOQG/@@download/IGVFFI4077AOQG.fastq.gz",
"s3_uri": "s3://igvf-files/2023/12/05/bb57a172-4f72-4153-9e84-02dd2d1b4642/IGVFFI4077AOQG.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-FFrep2-BinC-PCRrep8_S272_R2_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI2266UYYN/",
"accession": "IGVFFI2266UYYN",
"aliases": [
"jesse-engreitz:230807S022-THP1-P153-Amp_PPIF_promoter-BioRep2-FFrep2-BinC-PCRrep8_R1"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2023-12-05T22:21:58.686785+00:00",
"file_format": "fastq",
"file_size": 4638698,
"href": "/sequence-files/IGVFFI2266UYYN/@@download/IGVFFI2266UYYN.fastq.gz",
"s3_uri": "s3://igvf-files/2023/12/05/bffcbb2b-4504-4762-8002-4ad0fe8329dc/IGVFFI2266UYYN.fastq.gz",
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"term_name": "Illumina NextSeq 550"
},
"status": "released",
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"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI0800EEXN/",
"accession": "IGVFFI0800EEXN",
"aliases": [
"jesse-engreitz:230807S022-THP1-P153-Amp_PPIF_promoter-BioRep2-FFrep2-BinC-PCRrep4_R2"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2023-12-05T22:19:44.366950+00:00",
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"file_size": 5551908,
"href": "/sequence-files/IGVFFI0800EEXN/@@download/IGVFFI0800EEXN.fastq.gz",
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"term_name": "Illumina NextSeq 550"
},
"status": "released",
"submitted_file_name": "230807S022-THP1-P153-Amp_PPIF_promoter-BioRep2-FFrep2-BinC-PCRrep4_S268_R2_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI5299LSFY/",
"accession": "IGVFFI5299LSFY",
"aliases": [
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],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2023-12-05T22:19:17.759894+00:00",
"file_format": "fastq",
"file_size": 1360833,
"href": "/sequence-files/IGVFFI5299LSFY/@@download/IGVFFI5299LSFY.fastq.gz",
"s3_uri": "s3://igvf-files/2023/12/05/f45c7934-279b-430c-9376-646fdc956547/IGVFFI5299LSFY.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-FFrep2-BinC-PCRrep4_S268_I1_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI9825WHZM/",
"accession": "IGVFFI9825WHZM",
"aliases": [
"jesse-engreitz:230807S022-THP1-P153-Amp_PPIF_promoter-BioRep2-FFrep2-BinC-PCRrep7_I1"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2023-12-05T22:21:02.507651+00:00",
"file_format": "fastq",
"file_size": 1417367,
"href": "/sequence-files/IGVFFI9825WHZM/@@download/IGVFFI9825WHZM.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-FFrep2-BinC-PCRrep7_S271_I1_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI5190IWYZ/",
"accession": "IGVFFI5190IWYZ",
"aliases": [
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],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2023-12-05T22:22:33.931565+00:00",
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"href": "/sequence-files/IGVFFI5190IWYZ/@@download/IGVFFI5190IWYZ.fastq.gz",
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},
"status": "released",
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"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI1411ARZI/",
"accession": "IGVFFI1411ARZI",
"aliases": [
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],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2023-12-05T22:20:19.053238+00:00",
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"file_size": 5588509,
"href": "/sequence-files/IGVFFI1411ARZI/@@download/IGVFFI1411ARZI.fastq.gz",
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},
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"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI0767UQNW/",
"accession": "IGVFFI0767UQNW",
"aliases": [
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],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2023-12-05T22:17:24.210279+00:00",
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"term_name": "Illumina NextSeq 550"
},
"status": "released",
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"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI1236IUVB/",
"accession": "IGVFFI1236IUVB",
"aliases": [
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],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2023-12-05T22:15:56.525965+00:00",
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"href": "/sequence-files/IGVFFI1236IUVB/@@download/IGVFFI1236IUVB.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-FFrep2-BinC-PCRrep1_S265_I2_001.fastq.gz",
"upload_status": "validated"
},
{
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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": "c72d068b-98e8-4a24-adaf-7c5879e3c53b"
}