{
"@context": "/terms/",
"@id": "/measurement-sets/IGVFDS8504HJPW/",
"@type": [
"MeasurementSet",
"FileSet",
"Item"
],
"accession": "IGVFDS8504HJPW",
"aliases": [
"jesse-engreitz:230531S019-THP1-P151-Amp_PPIF_enhancer-BioRep2-FFrep1-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 [IGVFSM0841TQDY](/in-vitro-systems/IGVFSM0841TQDY/) has in progress subobject construct library set [IGVFDS2374NXLW](/construct-library-sets/IGVFDS2374NXLW/).",
"level": 30,
"level_name": "INTERNAL_ACTION",
"name": "audit_item_status",
"path": "/in-vitro-systems/IGVFSM0841TQDY/"
},
{
"category": "missing publication",
"detail": "In vitro system [IGVFSM0841TQDY](/in-vitro-systems/IGVFSM0841TQDY/) 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/IGVFSM0841TQDY/"
},
{
"category": "missing publication",
"detail": "Measurement set [IGVFDS8504HJPW](/measurement-sets/IGVFDS8504HJPW/) 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/IGVFDS8504HJPW/"
},
{
"category": "missing sequencing kit",
"detail": "Measurement set [IGVFDS8504HJPW](/measurement-sets/IGVFDS8504HJPW/) has sequence file(s) [IGVFFI3420FNUL](/sequence-files/IGVFFI3420FNUL/), [IGVFFI1911BMFU](/sequence-files/IGVFFI1911BMFU/), [IGVFFI6184JBOY](/sequence-files/IGVFFI6184JBOY/), [IGVFFI4641NUDK](/sequence-files/IGVFFI4641NUDK/), [IGVFFI0818OYSO](/sequence-files/IGVFFI0818OYSO/), [IGVFFI2232OBND](/sequence-files/IGVFFI2232OBND/), [IGVFFI9822TLTF](/sequence-files/IGVFFI9822TLTF/), [IGVFFI6845EQGG](/sequence-files/IGVFFI6845EQGG/), [IGVFFI4165IHQU](/sequence-files/IGVFFI4165IHQU/), [IGVFFI0537RBSY](/sequence-files/IGVFFI0537RBSY/), [IGVFFI6937SCLP](/sequence-files/IGVFFI6937SCLP/), [IGVFFI0328TTPZ](/sequence-files/IGVFFI0328TTPZ/), [IGVFFI6851UEAY](/sequence-files/IGVFFI6851UEAY/), [IGVFFI6325ZJYX](/sequence-files/IGVFFI6325ZJYX/), [IGVFFI3120AKPC](/sequence-files/IGVFFI3120AKPC/), [IGVFFI2997QKPV](/sequence-files/IGVFFI2997QKPV/), [IGVFFI0000LSBR](/sequence-files/IGVFFI0000LSBR/), [IGVFFI6178DYAU](/sequence-files/IGVFFI6178DYAU/), [IGVFFI6647ECDQ](/sequence-files/IGVFFI6647ECDQ/), [IGVFFI1697YVUG](/sequence-files/IGVFFI1697YVUG/), [IGVFFI7211NZTF](/sequence-files/IGVFFI7211NZTF/), [IGVFFI5123FNRM](/sequence-files/IGVFFI5123FNRM/), [IGVFFI0952NXHP](/sequence-files/IGVFFI0952NXHP/), [IGVFFI2399XUOF](/sequence-files/IGVFFI2399XUOF/), [IGVFFI2001HZEN](/sequence-files/IGVFFI2001HZEN/), [IGVFFI2537SZHL](/sequence-files/IGVFFI2537SZHL/), [IGVFFI8225GSHC](/sequence-files/IGVFFI8225GSHC/), [IGVFFI6293JLMF](/sequence-files/IGVFFI6293JLMF/), [IGVFFI7652YXOS](/sequence-files/IGVFFI7652YXOS/), [IGVFFI8421JDKR](/sequence-files/IGVFFI8421JDKR/), [IGVFFI7627ESHC](/sequence-files/IGVFFI7627ESHC/), [IGVFFI3724TACC](/sequence-files/IGVFFI3724TACC/), [IGVFFI4302BDGU](/sequence-files/IGVFFI4302BDGU/), [IGVFFI4922OUMR](/sequence-files/IGVFFI4922OUMR/), [IGVFFI4941PTZU](/sequence-files/IGVFFI4941PTZU/), [IGVFFI1963JVTJ](/sequence-files/IGVFFI1963JVTJ/), [IGVFFI8413UPDY](/sequence-files/IGVFFI8413UPDY/), [IGVFFI8323HXWT](/sequence-files/IGVFFI8323HXWT/), [IGVFFI1973MBPX](/sequence-files/IGVFFI1973MBPX/), [IGVFFI2565SEAF](/sequence-files/IGVFFI2565SEAF/), [IGVFFI9129DQAA](/sequence-files/IGVFFI9129DQAA/), [IGVFFI6372RNHN](/sequence-files/IGVFFI6372RNHN/), [IGVFFI2971HLBD](/sequence-files/IGVFFI2971HLBD/), [IGVFFI0395YQWS](/sequence-files/IGVFFI0395YQWS/), [IGVFFI5700TLJV](/sequence-files/IGVFFI5700TLJV/), [IGVFFI0591WKKM](/sequence-files/IGVFFI0591WKKM/), [IGVFFI3960GRGF](/sequence-files/IGVFFI3960GRGF/), [IGVFFI0955GZSP](/sequence-files/IGVFFI0955GZSP/) 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/IGVFDS8504HJPW/"
},
{
"category": "missing sequence specification",
"detail": "Measurement set [IGVFDS8504HJPW](/measurement-sets/IGVFDS8504HJPW/) has sequence file(s): [IGVFFI3420FNUL](/sequence-files/IGVFFI3420FNUL/), [IGVFFI1911BMFU](/sequence-files/IGVFFI1911BMFU/), [IGVFFI6184JBOY](/sequence-files/IGVFFI6184JBOY/), [IGVFFI4641NUDK](/sequence-files/IGVFFI4641NUDK/), [IGVFFI0818OYSO](/sequence-files/IGVFFI0818OYSO/), [IGVFFI2232OBND](/sequence-files/IGVFFI2232OBND/), [IGVFFI9822TLTF](/sequence-files/IGVFFI9822TLTF/), [IGVFFI6845EQGG](/sequence-files/IGVFFI6845EQGG/), [IGVFFI4165IHQU](/sequence-files/IGVFFI4165IHQU/), [IGVFFI0537RBSY](/sequence-files/IGVFFI0537RBSY/), [IGVFFI6937SCLP](/sequence-files/IGVFFI6937SCLP/), [IGVFFI0328TTPZ](/sequence-files/IGVFFI0328TTPZ/), [IGVFFI6851UEAY](/sequence-files/IGVFFI6851UEAY/), [IGVFFI6325ZJYX](/sequence-files/IGVFFI6325ZJYX/), [IGVFFI3120AKPC](/sequence-files/IGVFFI3120AKPC/), [IGVFFI2997QKPV](/sequence-files/IGVFFI2997QKPV/), [IGVFFI0000LSBR](/sequence-files/IGVFFI0000LSBR/), [IGVFFI6178DYAU](/sequence-files/IGVFFI6178DYAU/), [IGVFFI6647ECDQ](/sequence-files/IGVFFI6647ECDQ/), [IGVFFI1697YVUG](/sequence-files/IGVFFI1697YVUG/), [IGVFFI7211NZTF](/sequence-files/IGVFFI7211NZTF/), [IGVFFI5123FNRM](/sequence-files/IGVFFI5123FNRM/), [IGVFFI0952NXHP](/sequence-files/IGVFFI0952NXHP/), [IGVFFI2399XUOF](/sequence-files/IGVFFI2399XUOF/), [IGVFFI2001HZEN](/sequence-files/IGVFFI2001HZEN/), [IGVFFI2537SZHL](/sequence-files/IGVFFI2537SZHL/), [IGVFFI8225GSHC](/sequence-files/IGVFFI8225GSHC/), [IGVFFI6293JLMF](/sequence-files/IGVFFI6293JLMF/), [IGVFFI7652YXOS](/sequence-files/IGVFFI7652YXOS/), [IGVFFI8421JDKR](/sequence-files/IGVFFI8421JDKR/), [IGVFFI7627ESHC](/sequence-files/IGVFFI7627ESHC/), [IGVFFI3724TACC](/sequence-files/IGVFFI3724TACC/), [IGVFFI4302BDGU](/sequence-files/IGVFFI4302BDGU/), [IGVFFI4922OUMR](/sequence-files/IGVFFI4922OUMR/), [IGVFFI4941PTZU](/sequence-files/IGVFFI4941PTZU/), [IGVFFI1963JVTJ](/sequence-files/IGVFFI1963JVTJ/), [IGVFFI8413UPDY](/sequence-files/IGVFFI8413UPDY/), [IGVFFI8323HXWT](/sequence-files/IGVFFI8323HXWT/), [IGVFFI1973MBPX](/sequence-files/IGVFFI1973MBPX/), [IGVFFI2565SEAF](/sequence-files/IGVFFI2565SEAF/), [IGVFFI9129DQAA](/sequence-files/IGVFFI9129DQAA/), [IGVFFI6372RNHN](/sequence-files/IGVFFI6372RNHN/), [IGVFFI2971HLBD](/sequence-files/IGVFFI2971HLBD/), [IGVFFI0395YQWS](/sequence-files/IGVFFI0395YQWS/), [IGVFFI5700TLJV](/sequence-files/IGVFFI5700TLJV/), [IGVFFI0591WKKM](/sequence-files/IGVFFI0591WKKM/), [IGVFFI3960GRGF](/sequence-files/IGVFFI3960GRGF/), [IGVFFI0955GZSP](/sequence-files/IGVFFI0955GZSP/) 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/IGVFDS8504HJPW/"
}
],
"WARNING": [
{
"category": "missing auxiliary set",
"detail": "Measurement set [IGVFDS8504HJPW](/measurement-sets/IGVFDS8504HJPW/) 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/IGVFDS8504HJPW/"
}
]
},
"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/IGVFDS2374NXLW/",
"accession": "IGVFDS2374NXLW",
"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/IGVFDS4989HPTW/",
"accession": "IGVFDS4989HPTW",
"aliases": [
"jesse-engreitz:230531S019-THP1-P151-Amp_PPIF_enhancer-THP1-PE2_Exp1_NegControl_AmpliconSequencing"
],
"status": "released"
}
],
"control_for": [],
"creation_timestamp": "2023-11-30T22:49:08.596460+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/IGVFFI3420FNUL/",
"accession": "IGVFFI3420FNUL",
"aliases": [
"jesse-engreitz:230531S019-THP1-P151-Amp_PPIF_enhancer-BioRep2-FFrep1-BinA-PCRrep6_R1"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2023-12-05T21:21:45.601372+00:00",
"file_format": "fastq",
"file_size": 3059071,
"href": "/sequence-files/IGVFFI3420FNUL/@@download/IGVFFI3420FNUL.fastq.gz",
"s3_uri": "s3://igvf-files/2023/12/05/72dc5b73-dbbc-4c5c-8e87-9bc500a21c0c/IGVFFI3420FNUL.fastq.gz",
"sequencing_platform": {
"@id": "/platform-terms/EFO_0008566/",
"status": "released",
"term_name": "Illumina NextSeq 550"
},
"status": "released",
"submitted_file_name": "230531S019-THP1-P151-Amp_PPIF_enhancer-BioRep2-FFrep1-BinA-PCRrep6_S198_R1_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI1911BMFU/",
"accession": "IGVFFI1911BMFU",
"aliases": [
"jesse-engreitz:230531S019-THP1-P151-Amp_PPIF_enhancer-BioRep2-FFrep1-BinA-PCRrep1_R2"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2023-12-05T21:16:55.175043+00:00",
"file_format": "fastq",
"file_size": 3600519,
"href": "/sequence-files/IGVFFI1911BMFU/@@download/IGVFFI1911BMFU.fastq.gz",
"s3_uri": "s3://igvf-files/2023/12/05/8b345351-4298-4232-847b-7df267ee3023/IGVFFI1911BMFU.fastq.gz",
"sequencing_platform": {
"@id": "/platform-terms/EFO_0008566/",
"status": "released",
"term_name": "Illumina NextSeq 550"
},
"status": "released",
"submitted_file_name": "230531S019-THP1-P151-Amp_PPIF_enhancer-BioRep2-FFrep1-BinA-PCRrep1_S193_R2_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI6184JBOY/",
"accession": "IGVFFI6184JBOY",
"aliases": [
"jesse-engreitz:230531S019-THP1-P151-Amp_PPIF_enhancer-BioRep2-FFrep1-BinA-PCRrep7_I1"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2023-12-05T21:22:04.352571+00:00",
"file_format": "fastq",
"file_size": 758223,
"href": "/sequence-files/IGVFFI6184JBOY/@@download/IGVFFI6184JBOY.fastq.gz",
"s3_uri": "s3://igvf-files/2023/12/05/c518682b-304f-44b2-a821-bfd66878998e/IGVFFI6184JBOY.fastq.gz",
"sequencing_platform": {
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"status": "released",
"term_name": "Illumina NextSeq 550"
},
"status": "released",
"submitted_file_name": "230531S019-THP1-P151-Amp_PPIF_enhancer-BioRep2-FFrep1-BinA-PCRrep7_S289_I1_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI4641NUDK/",
"accession": "IGVFFI4641NUDK",
"aliases": [
"jesse-engreitz:230531S019-THP1-P151-Amp_PPIF_enhancer-BioRep2-FFrep1-BinA-PCRrep7_R1"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2023-12-05T21:22:22.870007+00:00",
"file_format": "fastq",
"file_size": 2873968,
"href": "/sequence-files/IGVFFI4641NUDK/@@download/IGVFFI4641NUDK.fastq.gz",
"s3_uri": "s3://igvf-files/2023/12/05/2c5c7725-ec1f-4d51-8517-037d7ae16078/IGVFFI4641NUDK.fastq.gz",
"sequencing_platform": {
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"status": "released",
"term_name": "Illumina NextSeq 550"
},
"status": "released",
"submitted_file_name": "230531S019-THP1-P151-Amp_PPIF_enhancer-BioRep2-FFrep1-BinA-PCRrep7_S289_R1_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI0818OYSO/",
"accession": "IGVFFI0818OYSO",
"aliases": [
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],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2023-12-05T21:18:56.962300+00:00",
"file_format": "fastq",
"file_size": 843359,
"href": "/sequence-files/IGVFFI0818OYSO/@@download/IGVFFI0818OYSO.fastq.gz",
"s3_uri": "s3://igvf-files/2023/12/05/ceecd93e-4b4c-4beb-8699-206ea88922c5/IGVFFI0818OYSO.fastq.gz",
"sequencing_platform": {
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"status": "released",
"term_name": "Illumina NextSeq 550"
},
"status": "released",
"submitted_file_name": "230531S019-THP1-P151-Amp_PPIF_enhancer-BioRep2-FFrep1-BinA-PCRrep2_S194_I1_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI2232OBND/",
"accession": "IGVFFI2232OBND",
"aliases": [
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],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2023-12-05T21:21:36.326285+00:00",
"file_format": "fastq",
"file_size": 819827,
"href": "/sequence-files/IGVFFI2232OBND/@@download/IGVFFI2232OBND.fastq.gz",
"s3_uri": "s3://igvf-files/2023/12/05/45cb2713-68a5-4c4f-97a5-867fe12b0fc1/IGVFFI2232OBND.fastq.gz",
"sequencing_platform": {
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"status": "released",
"term_name": "Illumina NextSeq 550"
},
"status": "released",
"submitted_file_name": "230531S019-THP1-P151-Amp_PPIF_enhancer-BioRep2-FFrep1-BinA-PCRrep6_S198_I2_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI9822TLTF/",
"accession": "IGVFFI9822TLTF",
"aliases": [
"jesse-engreitz:230531S019-THP1-P151-Amp_PPIF_enhancer-BioRep2-FFrep1-BinA-PCRrep7_R2"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2023-12-05T21:22:32.138434+00:00",
"file_format": "fastq",
"file_size": 3468156,
"href": "/sequence-files/IGVFFI9822TLTF/@@download/IGVFFI9822TLTF.fastq.gz",
"s3_uri": "s3://igvf-files/2023/12/05/2e4a1596-4753-4b54-aa82-2a67f992ae87/IGVFFI9822TLTF.fastq.gz",
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"status": "released",
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},
"status": "released",
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"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI6845EQGG/",
"accession": "IGVFFI6845EQGG",
"aliases": [
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],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2023-12-05T21:17:04.591363+00:00",
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"file_size": 867919,
"href": "/sequence-files/IGVFFI6845EQGG/@@download/IGVFFI6845EQGG.fastq.gz",
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},
"status": "released",
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"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI4165IHQU/",
"accession": "IGVFFI4165IHQU",
"aliases": [
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],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2023-12-05T21:20:39.445465+00:00",
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"href": "/sequence-files/IGVFFI4165IHQU/@@download/IGVFFI4165IHQU.fastq.gz",
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"sequencing_platform": {
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"status": "released",
"term_name": "Illumina NextSeq 550"
},
"status": "released",
"submitted_file_name": "230531S019-THP1-P151-Amp_PPIF_enhancer-BioRep2-FFrep1-BinA-PCRrep4_S196_R2_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI0537RBSY/",
"accession": "IGVFFI0537RBSY",
"aliases": [
"jesse-engreitz:230531S019-THP1-P151-Amp_PPIF_enhancer-BioRep2-FFrep1-BinA-PCRrep12_I2"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2023-12-05T21:18:28.793094+00:00",
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"file_size": 811378,
"href": "/sequence-files/IGVFFI0537RBSY/@@download/IGVFFI0537RBSY.fastq.gz",
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},
"status": "released",
"submitted_file_name": "230531S019-THP1-P151-Amp_PPIF_enhancer-BioRep2-FFrep1-BinA-PCRrep12_S294_I2_001.fastq.gz",
"upload_status": "validated"
},
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},
"submitted_files_timestamp": "2023-12-05T21:16:27.678449+00:00",
"summary": "CRISPR prime editing Variant-EFFECTS sorted on the expression of PPIF integrating a guide (sgRNA) library targeting sequence variants in a genomic locus",
"targeted_genes": [
{
"@id": "/genes/ENSG00000108179/",
"geneid": "ENSG00000108179",
"name": "peptidylprolyl isomerase F",
"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": "ef5a9a11-b681-40fb-acb0-401964b44f23"
}