IRCMS provides to eligible students and interested staff of Kumamoto University access to its mini-cluster for bioinformatics research and education.
The four-node cluster has 80 cores. Two nodes consist of four standard Intel Xeon E5-2680 v4, 2.40 GHz 14-core processors, 32 DDR4 (2400 MHz) 32 GB memory modules and two NVIDIA Tesla K80 GPUs. The other two nodes are composed of four older Intel Xeon E5-2630 v2, 2.30 GHz 6-core processors, 48 DDR3 (1866 MHz) 16 GB memory modules and two NIVIDA Quadro K4000 GPUs. A tape library system is used for archiving. A G-SPEED Studio XL 42 TB storage server that is mounted to the front-end of the cluster facilates data transfer from PCs linked with instruments to the storage server and access of the stored data from the cluster or networked PCs.
Users are permitted to install their own tools in their home directory and create web-accessible databases. General available tools and packages include AmberTools, Bioconductor, BioPerl, BioRuby, Bowtie2, Cytoscape, HMMER, GATK, MODELLER, MySQL, NCBI toolkit, Perl, PHP, PyMOL, Python, RStudio Server, Tophat2, SAMtools, and Trinity among others.
Single cell transcriptome
To perform single-cell RNA sequencing, revrese transcription and DNA amplification are necessary. We provide Single Cell Reverse Transcription with Random Displacement Amplification (scRT- RamDA) method. This method enables a 10-100 fold increase in cDNA yield, the highest reproducibility, accuracy, and full-length coverage across transcripts. By using this new technology, you can cyclopedically analyze the transcriptional product in one cell.
For inquiries on collaborative research contact Ryoko Koitabashi r_koitabashi [at] kumamoto-u.ac.jp
Single cell proteomics
We provide services of single cell proteomics using the Helios, a CyTOF System for mass spectrometry. The Helios system has 135 detection channels and is able to measure more than 40 markers per cell. Cellular targets are labeled with metal-tagged antibodies. Then they are detected and quantified by time- of -flight mass spectrometry. The high qurity and choice of metal isotopes provide minimal signal overlap.
This system enables you to fully study the functional complexity of biological systems at the single-cell level.
For inquiries on collaborative research contact Akifumi Kiyota a-kiyota [at] kumamoto-u.ac.jp