Affiliation: RIKEN Brain Science Institute
- Population transcriptomics with single-cell resolution: a new field made possible by microfluidics: a technology for high throughput transcript counting and data-driven definition of cell typesCharles Plessy
RIKEN Omics Science Center, Suehiro cho, Tsurumi ku, Yokohama, Japan
Bioessays 35:131-40. 2013....
- Linking promoters to functional transcripts in small samples with nanoCAGE and CAGEscanCharles Plessy
RIKEN Yokohama Institute, Omics Science Center, Yokohama, Japan
Nat Methods 7:528-34. 2010..Both of these methods allow further annotation-agnostic studies of the complex human transcriptome...
- Promoter architecture of mouse olfactory receptor genesCharles Plessy
RIKEN Yokohama Institute, Omics Science Center, Yokohama, Kanagawa, Japan
Genome Res 22:486-97. 2012..Finally, we showed that a short genomic fragment flanking the major TSS of the OR gene Olfr160 (M72) can drive OSN-specific expression in transgenic mice...
- Suppression of artifacts and barcode bias in high-throughput transcriptome analyses utilizing template switchingDave T P Tang
Omics Science Center, RIKEN Yokohama Institute, 1 7 22 Suehiro cho, Yokohama, Kanagawa 230 0045, Japan
Nucleic Acids Res 41:e44. 2013..We describe a strategy that eliminates these artifacts in silico and propose an experimental solution that suppresses biases from TS...
- Comparison of RNA- or LNA-hybrid oligonucleotides in template-switching reactions for high-speed sequencing library preparationMatthias Harbers
RIKEN Center for Life Science Technologies, Division of Genomics Technologies, Yokohama, Kanagawa 230 0045, Japan
BMC Genomics 14:665. 2013..Adding template-switching oligonucleotides to reverse transcription reactions is the most commonly used approach when working with very small quantities of RNA even from single cells...
- NanoCAGE: a high-resolution technique to discover and interrogate cell transcriptomesMd Salimullah
RIKEN Yokohama Institute, Omics Science Center, Yokohama City, Kanagawa, 230 0045, Japan
Cold Spring Harb Protoc 2011:pdb.prot5559. 2011..The libraries can be sequenced using an Illumina sequencer Genome Analyzer IIX [corrected] with a level of sensitivity 1000 times higher than CAGE...
- Tunable fractionation of nucleic acidsMd Salimullah
Functional Genomics Technology Team, Omics Science Center OSC, RIKEN Yokohama Institute, Kanagawa, Japan
Biotechniques 47:1041-3. 2009..This method could also be applied to the fractionation of nucleic acids generated by other types of reactions...
- High-throughput verification of transcriptional starting sites by Deep-RACESigne Olivarius
Functional Genomics Technology Team, Omics Science Center, RIKEN Yokohama Institute, Kanagawa, Japan
Biotechniques 46:130-2. 2009..In comparison to the sequencing of RACE PCR products, our approach is more precise and more cost-effective even for batches as small as 17...
- A resource for transcriptomic analysis in the mouse brainCharles Plessy
Functional Genomics Technology Team, Omics Science Center, RIKEN Yokohama Institute, Yokohama, Kanagawa, Japan
PLoS ONE 3:e3012. 2008..Studies of sorted cells expressing the same transgene have shown that cell populations can be distinguished according to their transcriptional profile...
- The transcriptional network that controls growth arrest and differentiation in a human myeloid leukemia cell lineHarukazu Suzuki
RIKEN Omics Science Center, RIKEN Yokohama Institute, Kanagawa, Japan
Nat Genet 41:553-62. 2009....