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GEO help: Mouse over screen elements for information. |
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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
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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.
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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.
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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 |
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Submission date |
Dec 06, 2018 |
Last update date |
Apr 20, 2022 |
Contact name |
Allen Institute |
Organization name |
The Allen Institute for Brain Science
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Street address |
615 Westlake Ave N
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City |
Seattle |
State/province |
WA |
ZIP/Postal code |
98109 |
Country |
USA |
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Platforms (1) |
GPL17021 |
Illumina HiSeq 2500 (Mus musculus) |
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Samples (956)
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Relations |
BioProject |
PRJNA508779 |
SRA |
SRP172768 |
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 |
SRA Run Selector |
Raw data are available in SRA |
Processed data are available on Series record |
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