Itoshi NIKAIDO

"scRepli-RamDA-seq" is out in Nat Commun! A collaboration combining scRepli-seq (Hiratani Lab.), nuclear isolation (Hirabayashi Lab.), & our scRamDA-seq. We achieved high-res DNA replication & full-length Total RNA profiling from the same single cell! nature.com/articles/s4146…

Our scRR-seq paper is out! Congrats to Rawin Poonperm, Taiki Yoneda, Shin-ichiro Takebayashi, and everyone involved! We successfully combined Itoshi Nikaido’s RamDA-seq (single-cell RNA-seq) with our scRepli-seq technology. nature.com/articles/s4146…

Huge thanks for the SCODE acceleration! Amazing job! 👍

Merging these unique technologies opens new doors. Our simplified protocol utilizes the RamDA-seq kit from #TOYOBO, making it user-friendly. We hope this robust multi-omics tool fuels your new discoveries! Code & data below. nature.com/articles/s4146…

It empowers haplotype-specific analysis! We directly linked allelic RT asynchrony to expression imbalance in single cells. We can also correlate replication stress-induced CNVs with gene expression changes to study genome instability.

"scRepli-RamDA-seq" is out in Nat Commun! A collaboration combining scRepli-seq (Hiratani Lab.), nuclear isolation (Hirabayashi Lab.), & our scRamDA-seq. We achieved high-res DNA replication & full-length Total RNA profiling from the same single cell! nature.com/articles/s4146…

Study uncovers the secrets of plant regeneration phys.org/news/2023-07-u…

How are cell fates specified in heterogeneous callus cell population undergoing shoot regeneration? We tackled this long-standing question using Quartz-Seq2 and by focusing on two WOX TFs. Check out our latest publication in @ScienceAdvances! science.org/doi/10.1126/sc…

Single-Cell Sequencing Approach Homes in on Signaling Pathway in Gastric Cell Differentiation . A Nature Communications paper reports that EGFR-ERK signaling promotes differentiation, while NF-κB signaling promotes an undifferentiated state among... ow.ly/VLGU104MoM1

We experimentally verified that TGFα signaling promotes stem cell differentiation into pit cells, while TNFSF12 signaling maintains progenitor cells. (5/n)

Based on the results, we have discovered factors that enhance or inhibit differentiation-regulated signals using gastric epithelial organoids from 3D cultures of stem cells. (4/n)

We are excited to share a paper that uncovers one aspect of the regulatory mechanism of stem cell differentiation that protects the gastric mucosa. (1/n) nature.com/articles/s4146…

scTensor detects many-to-many cell-cell interactions from single cell RNA-sequencing data biorxiv.org/cgi/content/sh… #bioRxiv

We propose a novel deep learning model that can predict epitope-MHC class II binding from limited training data. Our MTL4MHC2 consists of multi-task Bi-LSTM models, an antigen peptide learning model and an MHC peptide learning model. researchgate.net/publication/36…

This research was accomplished through the efforts of Prof. Okada, Ms. Wibisana and colleagues. Our lab was in charge of scRNA-seq experiments using RamDA-seq.

Wibisana et al suggest that transcription factor NF-κB super-enhancers have an important role in the transcriptional regulation of B cells 🔎: doi.org/10.1371/journa… @dritoshi @dritoshien @cellsystems_ipr @IPR_pr @RIKEN_IMS #CellBiology #Genetics #chromatin

@jnicolausw @cellsystems_ipr @PLOSGenetics Congratulations!

Happy to announce that our research during my work at @cellsystems_ipr is finally published in @PLOSGenetics : Enhanced transcriptional heterogeneity mediated by NF-κB super-enhancers dx.plos.org/10.1371/journa…