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Series GSE38198 Query DataSets for GSE38198
Status Public on May 25, 2012
Title Tn5 transposase-mediated library preparation of single-cell cDNAs for RNA-seq
Organism Mus musculus
Experiment type Expression profiling by high throughput sequencing
Summary Deep sequencing of single cell-derived genomic DNA and/or cDNAs brings novel insights into oncogenesis and embryogenesis. However, traditional library preparation for RNA-Seq requires multiple steps, including shearing the target DNA/RNA and following sequential enzymatic reactions, which result in consequent sample loss and stochastic variation at each step. Such variation may significantly affect the output from sequencing. We have found that a new technique of library preparation using hyperactive Tn5 transposase for the next-generation sequencer of Illumina's platform provided high-quality libraries from 100ng of short-length (average 700~800 bp) single-cell level cDNA. This new method reduced the number of steps in the protocol, which resulted in improved reproducibility and reduced variation among the specimens.
Overall design Two methods of library preparation (sonication, tagmentation with hyperactive Tn5 transposase) were compared in the case of RNA-Seq for single-cell level cDNA. Technical triplicates were used.
Contributor(s) Brouilette S, Kuersten S, Mein C, Bozek M, Terry A, Dias KR, Bhaw-Rosun L, Shintani Y, Coppen S, Ikebe C, Sawhney V, Campbell N, Kaneko M, Tano N, Ishida H, Suzuki K, Yashiro K
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Submission date May 23, 2012
Last update date May 15, 2019
Contact name Kenta Yashiro
Phone +44 (0)20 7882 8235
Organization name Barts and The London School of Medicine and Dentistry, Queen Mary University of London
Department Willaim Harvey research Institute
Lab Translational Medicine and Therapeutics
Street address Charterhouse Square
City London
ZIP/Postal code EC1M 6BQ
Country United Kingdom
Platforms (1)
GPL11002 Illumina Genome Analyzer IIx (Mus musculus)
Samples (6)
GSM936484 Sonicated single-cell level cDNA #1
GSM936485 Sonicated single-cell level cDNA #2
GSM936486 Sonicated single-cell level cDNA #3
SRA SRP013380
BioProject PRJNA167516

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Supplementary file Size Download File type/resource
GSE38198_single_cell_level_cDNA_of_ESCs_RPKM.txt.gz 279.6 Kb (ftp)(http) TXT
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