Snowing Hershey… again!

The town has been covered in white almost all the time this winter.

Moving from CT, who could have expected this much of snow in PA!

Anyhow, today I introduced ENCODE best practice documents to one of our customers.

https://genome.ucsc.edu/ENCODE/protocols/dataStandards/

Good stuffs to read and follow when you are new to the ChIP-seq/RNA-seq fields.

In this week and the following, I will be working on several ChIP-seq and RNA-seq projects!

This was obviously the biggest news of this week!

HiSeq X Ten is on sell at $1M per machine. You have to buy 10 (That’s for “X” and “Ten”) machines and you can sequence only human genome (no other species). 3 institutes purchased this including Broad. Will they be accepting small external projects from someone like me? 🙂

http://nextgenseek.com/2014/01/illumina-announces-new-sequencers-hiseqx-nextseq-500-at-jpm-2014/

-Yuka

I receive this type of question many times. What is the best way to extract RNA for sequencing? And here is what I would recommend:

1. Trizol is always the best choice as a reagent. Ambion’s ToTTALLY RNA and MirVana are also great. Qiagen columns will get rid of smaller RNAs so would not recommend unless you don’t care for those small stuffs (ncRNAs).

2. We have QIASymphony and I would use this for DNA isolation, but for RNA, because the smaller RNAs will be gone after QIASymphony prep, I would use classic homogenizer to lyse the tissue/cells (fyi, QIASymphony has different protocol for isolating miRNA enriched RNA).

3. I would recommend using higher throughput (robot-type) devices to avoid cross-contamination and sample loss, and here we have Bullet Blender, the little rice-cooker type of machine you can buy at <$3,000. You mix small beads and lysis buffer to your tissue (I do this on dry ice) and let them shaken crazy within this rice-cooker for 1 min and your lysis is done! I actually warm up the tube at 37C for a few minutes after the 1st blending and then blend again for 1 min to ensure guanidine-type of lysis buffer to penetrate well within the cell: at lower temp, it doesn’t penetrate well so you will not get full recovery of your RNA! 🙁

We have Bullet Blender at our core, and any investigators are welcome to use it by contributing small $ to the consumables (beads and safe-lock tubes).

http://www.nextadvance.com/api/index.cfm/products.info/c/421/Bullet-Blender#/Overview

Contact me anytime for the instruction how to use our “little RNA-cooker” 🙂

-Yuka

One of my papers from Yale/Sestan lab (www.sestanlab.org), so called “cortical map” paper, is just out!

Congrats to Miha, Andre, and Goran: the talented cortical gangs in the Sestan lab!

-Yuka

http://www.ncbi.nlm.nih.gov/pubmed/24373884

Neuron. 2013 Dec 24. pii: S0896-6273(13)01086-6. doi: 10.1016/j.neuron.2013.11.018. [Epub ahead of print]

Temporal Specification and Bilaterality of Human Neocortical Topographic Gene Expression.

Pletikos M¹, Sousa AM², Sedmak G¹, Meyer KA³, Zhu Y³, Cheng F⁴, Li M³, Kawasawa YI³, Sestan N⁵.

Abstract

Transcriptional events involved in the development of human cerebral neocortex are poorly understood. Here, we analyzed the temporal dynamics and laterality of gene expression in human and macaque monkey neocortex. We found that interareal differences exhibit a temporal hourglass pattern, dividing the human neocortical development into three major phases. The first phase, corresponding to prenatal development, is characterized by the highest number of differential expressed genes among areas and gradient-like expression patterns, including those that are different between human and macaque. The second, preadolescent phase, is characterized by lesser interareal expression differences and by an increased synchronization of areal transcriptomes. During the third phase, from adolescence onward, differential expression among areas increases again driven predominantly by a subset of areas, without obvious gradient-like patterns. Analyses of left-right gene expression revealed population-level global symmetry throughout the fetal and postnatal time span. Thus, human neocortical topographic gene expression is temporally specified and globally symmetric.

 

Press release is available from here:

http://news.yale.edu/2013/12/26/human-brain-development-symphony-three-movements

I started my new career as a director at Genome Science Core at Penn State Hershey in Aug 2013. I am thrilled to grow as a team and stimulate cutting-edge genomics and translational research. Any inquiries or suggestions are always welcome! Thank you, Yuka