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Series GSE198951 Query DataSets for GSE198951
Status Public on Oct 19, 2022
Title Ambient RNA analysis reveals misinterpreted and masked cell types in brain single-nuclei datasets
Platform organism Homo sapiens
Sample organisms Homo sapiens; Mus musculus
Experiment type Expression profiling by high throughput sequencing
Third-party reanalysis
Summary Ambient RNA contamination in single-cell RNA sequencing (RNA-seq) is a significant problem, but its consequences are poorly understood. Here, we show that ambient RNAs in brain single-nuclei RNA-seq can have a nuclear or extra-nuclear origin, and each origin results in a distinct gene set signature. Both ambient RNA signatures are predominantly neuronal and we find that some previously annotated neuronal cell types are distinguished by ambient RNA. Strikingly, we also detect pervasive neuronal ambient RNA contamination in all glial cell types unless glia and neurons are physically separated prior to sequencing. We demonstrate that this contamination can be removed in silico using existing tools. We also show that previous annotations of immature oligodendrocytes are likely glial cells contaminated with ambient RNAs. After ambient RNA removal, we can detect extremely rare committed oligodendrocyte progenitor cells, which were infrequently annotated in previously published adult human brain datasets. Together, these results provide an in-depth analysis of ambient RNA contamination in brain single-cell datasets.
 
Overall design Data were reanalzyzed from raw fastq files with or without CellBender. Cells were annotated based on their cell type and glial cells were additionally annotated for ambient RNA contamination based on ambient RNA marker gene enrichment. Oligodendrocyte progenitor cells were additionally clustered and annotated.
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Reanalyzed data includes PRJNA434002 (SRR9262927-SRR9262957), GSE192773, GSE97930, and GSE198640)
 
Contributor(s) Caglayan E, Liu Y, Konopka G
Citation(s) 36240767
Submission date Mar 18, 2022
Last update date Oct 19, 2022
Contact name Genevieve Konopka
E-mail(s) genevieve.konopka@utsouthwestern.edu
Organization name University of Texas Southwestern Medical Center
Department Neuroscience
Lab Konopka
Street address 5323 Harry Hines Blvd.
City Dallas
State/province Texas
ZIP/Postal code 75390
Country USA
 
Platforms (2)
GPL16791 Illumina HiSeq 2500 (Homo sapiens)
GPL24676 Illumina NovaSeq 6000 (Homo sapiens)
Samples (4)
GSM6428209 NSD2_1
GSM6428210 NSD2_2
GSM6428211 NSD2_3
Relations
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Reanalysis of GSM5954175
Reanalysis of GSM5954176
BioProject PRJNA865472

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Supplementary file Size Download File type/resource
GSE198951_NSD1_CellBender_Glia.RDS.gz 141.6 Mb (ftp)(http) RDS
GSE198951_NSD1_NoCellBender_Glia.RDS.gz 159.5 Mb (ftp)(http) RDS
GSE198951_NSD1_OPC_Seurat.RDS.gz 1.8 Gb (ftp)(http) RDS
GSE198951_NSD1_intronicRatios.txt.gz 15.5 Mb (ftp)(http) TXT
GSE198951_NSD2_CellBender_Glia.RDS.gz 41.7 Mb (ftp)(http) RDS
GSE198951_NSD2_NoCellBender_Glia.RDS.gz 560.5 Mb (ftp)(http) RDS
GSE198951_NSD2_OPC_Seurat.RDS.gz 89.3 Mb (ftp)(http) RDS
GSE198951_NSD2_intronicRatios.txt.gz 1.4 Mb (ftp)(http) TXT
GSE198951_README_GEO.txt 757 b (ftp)(http) TXT
GSE198951_SD1_CellBender_Glia.RDS.gz 13.9 Mb (ftp)(http) RDS
GSE198951_SD1_NoCellBender_Glia.RDS.gz 16.7 Mb (ftp)(http) RDS
GSE198951_SD1_OPC_Seurat.RDS.gz 24.7 Mb (ftp)(http) RDS
GSE198951_SD1_intronicRatios.txt.gz 1.1 Mb (ftp)(http) TXT
GSE198951_SD2_CellBender_Glia.RDS.gz 114.5 Mb (ftp)(http) RDS
GSE198951_SD2_NoCellBender_Glia.RDS.gz 26.0 Mb (ftp)(http) RDS
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Raw data not applicable for this record
Processed data provided as supplementary file

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