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Series GSE123454 Query DataSets for GSE123454
Status Public on Dec 06, 2018
Title Single-nucleus and single-cell transcriptomes compared in matched cortical cell types
Organism Mus musculus
Experiment type Expression profiling by high throughput sequencing
Summary Transcriptomic profiling of complex tissues by single-nucleus RNA-sequencing (snRNA-seq) affords some advantages over single-cell RNA-sequencing (scRNA-seq). snRNA-seq provides less biased cellular coverage, does not appear to suffer cell isolation-based transcriptional artifacts, and can be applied to archived frozen specimens. We used well-matched snRNA-seq and scRNA-seq datasets from mouse visual cortex to compare cell type detection. Although more transcripts are detected in individual whole cells (~11,000 genes) than nuclei (~7,000 genes), we demonstrate that closely related neuronal cell types can be similarly discriminated with both methods if intronic sequences are included in snRNA-seq analysis. We estimate that the nuclear proportion of total cellular mRNA varies from 20% to over 50% for large and small pyramidal neurons, respectively. Together, these results illustrate the high information content of nuclear RNA for characterization of cellular diversity in brain tissues.
 
Overall design scRNA-seq of 463 single nuclei and 463 matched single cells from mouse primary visual cortex (VISp) and 30 control samples. Note that single cell data respresents a small subset of VISp cells from GEO series GSE115746.
 
Contributor(s) Bakken TE, Hodge RD, Miller JA, Yao Z, Nguyen TN, Aevermann B, Barkan E, Bertagnolli D, Casper T, Dee N, Garren E, Goldy J, Graybuck LT, Kroll M, Lasken RS, Lathia K, Parry S, Rimorin C, Scheuermann RH, Schork NJ, Shehata SI, Tieu M, Phillips JW, Bernard A, Smith KA, Zeng H, Lein ES, Tasic B
Citation(s) 30586455
Submission date Dec 06, 2018
Last update date Apr 20, 2022
Contact name Allen Institute
Organization name The Allen Institute for Brain Science
Street address 615 Westlake Ave N
City Seattle
State/province WA
ZIP/Postal code 98109
Country USA
 
Platforms (1)
GPL17021 Illumina HiSeq 2500 (Mus musculus)
Samples (956)
GSM3503373 LS-15045_S01_E1-50
GSM3503374 LS-15045_S02_E1-50
GSM3503375 LS-15045_S03_E1-50
Relations
BioProject PRJNA508779
SRA SRP172768

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Supplementary file Size Download File type/resource
GSE123454_GEO_seq_template_v2.1_Nuc_vs_Cell.xls.gz 164.8 Kb (ftp)(http) XLS
GSE123454_cells_exon_counts.csv.gz 6.7 Mb (ftp)(http) CSV
GSE123454_cells_intron_counts.csv.gz 4.7 Mb (ftp)(http) CSV
GSE123454_controls_exon_counts.csv.gz 484.5 Kb (ftp)(http) CSV
GSE123454_controls_intron_counts.csv.gz 318.7 Kb (ftp)(http) CSV
GSE123454_nuclei_exon_counts.csv.gz 4.7 Mb (ftp)(http) CSV
GSE123454_nuclei_intron_counts.csv.gz 4.4 Mb (ftp)(http) CSV
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Raw data are available in SRA
Processed data are available on Series record

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