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Series GSE56638 Query DataSets for GSE56638
Status Public on May 21, 2015
Title Deep sequencing reveals cell-type specific patterns of single cell transcriptome variation
Organisms Mus musculus; Rattus norvegicus
Experiment type Expression profiling by high throughput sequencing
Summary We present high quality deep read-depth single cell RNA sequencing for 91 cells from five mouse tissues and 18 cells from two rat tissues, along with 30 control samples of bulk RNA diluted to single-cell levels. We find that transcriptomes differ globally across tissues with regard to the number of genes expressed, the average expression patterns, and within cell-type variation patterns. We develop methods to filter genes for reliable quantification and to calibrate biological variation. All cell types include genes with high variability in expression, in a tissue-specific manner. We also find evidence that single cell variability of neuronal genes in mice is correlated with that in rats consistent with the hypothesis that levels of variation may be conserved.
Overall design From an initial 143 cells we identified 107 high quality samples with deep genic coverage, including 13 brown adipocytes, 19 cardiomyocytes, 19 cortical pyramidal neurons and 18 hippocampal pyramidal neurons from embryonic mouse, 8 cortical pyramidal neurons and 8 hippocampal pyramidal neurons from embryonic rat, and 22 serotonergic neurons from adult mouse. While mouse data is collected from three strains of mice at different ages, each cell type dataset is internally consistent. There are no technical replicates of single-cell samples. We additionally prepared 30 control samples, amplifications of bulk total cardiomyocyte RNA diluted to single cell quantities.
Contributor(s) Dueck H, Khaladkar M, Kim TK, Spaethling JM, Francis C, Suresh S, Fisher S, Seale P, Beck SG, Bartfai T, Kuhn B, Eberwine J, Kim J
Citation(s) 26056000
Submission date Apr 09, 2014
Last update date May 15, 2019
Contact name Junhyong Kim
Organization name University of Pennsylvania
Department Biology
Lab Junhyong Kim
Street address 433 S University Avenue
City Philadelphia
State/province PA
ZIP/Postal code 19104
Country USA
Platforms (3)
GPL13112 Illumina HiSeq 2000 (Mus musculus)
GPL14844 Illumina HiSeq 2000 (Rattus norvegicus)
GPL17021 Illumina HiSeq 2500 (Mus musculus)
Samples (137)
GSM1366181 BAT_1
GSM1366182 BAT_2
GSM1366183 BAT_3
BioProject PRJNA244374
SRA SRP041119

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Supplementary file Size Download File type/resource
GSE56638_RAW.tar 11.1 Mb (http)(custom) TAR (of TXT)
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file

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