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| 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.
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| |
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| 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.
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| 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 |
| Citation missing |
Has this study been published? Please login to update or notify GEO. |
| Submission date |
May 23, 2012 |
| Last update date |
May 15, 2019 |
| Contact name |
Kenta Yashiro |
| E-mail(s) |
k.yashiro@qmul.ac.uk
|
| 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 |
| |
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| Platforms (1) |
| GPL11002 |
Illumina Genome Analyzer IIx (Mus musculus) |
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| Samples (6)
|
| GSM936484 |
Sonicated single-cell level cDNA #1 |
| GSM936485 |
Sonicated single-cell level cDNA #2 |
| GSM936486 |
Sonicated single-cell level cDNA #3 |
| GSM936487 |
Tagmented single-cell level cDNA with Tn5 transposase #1 |
| GSM936488 |
Tagmented single-cell level cDNA with Tn5 transposase #2 |
| GSM936489 |
Tagmented single-cell level cDNA with Tn5 transposase #3 |
|
| Relations |
| SRA |
SRP013380 |
| BioProject |
PRJNA167516 |
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