Our mini-paper introducing iMate Protocol

The modified protocol from my unit is introduced in a mini-paper published online in the journal Biotechniques.


Optimization and cost-saving in tagmentation-based mate-pair library preparation and sequencing
Kaori Tatsumi, Osamu Nishimura, Kazu Itomi, Chiharu Tanegashima, and Shigehiro Kuraku
BioTechniques 58:253-257 (May 2015) doi 10.2144/000114288


Therein, we also introduce our strategy to get 80nt-long, 127nt-long or 171nt-long reads using only SBS kits for 50 cycles with HiSeq Rapid Run mode (v1).

Complicated! - lamprey genome resource availability

I have been asked by many of people around me about publicly available resources of the sea lamprey genome. I have just written down some facts and information on an independent new page inside this blog, titled 'Lamprey genome guide'. The situation is somewhat complicated, I see.

I will try to keep this page updated for the lamprey researchers' convenience.
I believe this third-party guide does not interfere any database function and research activity by other researchers. But, please let me know if there is some problem.

Croc genomes

A paper reporting results and plans of crocodile genome sequencing is out in Genome Biology.

The consortium page is here. One can also run BLAT searches at the UCSC site.

A course at NHGRI

I have just found a web page containing the schedule of a course running at NHGRI in US. The course is titled 'Current Topics In Genome Analysis 2012'. This should be a great overview of where we stand in genomics.

Report from 6th Intl Chick Meeting

As part of POULTRY GENOME NEWSLETTER posted in AnGenMap emailing list, I received a report from the 6th International Chicken Meeting.

 'The Sixth International Chicken Meeting, previously scheduled for Sendai, Japan, was held at the new Roslin Institute facility in Edinburgh, Scotland, September 17-20. Kudos to the outstanding organizational efforts of Dave Burt and his team (especially Liz Brown) from Roslin and thanks for their exceptional hospitality. Among the highlights: Wes Warren spoke of the on-going efforts to improve the chicken sequence assembly. He noted that the Galgal4 assembly was sent to browsers about 1.5 months ago and should be out soon, but there remains more to do to fill gaps and find missing microchromosome sequences. Almas Gheyas described the sequencing of 243 chickens, generating nearly 140M SNP and efforts to reduce this set to the most useful 675,000 SNP for a new Affymetrix genotyping array expected to be out middle of next year. There were several remarkable and even beautiful talks on cell labeling and imaging, and the use of these approaches to follow cell commitment and development pathways. Olivier Pourquie described the mechanism of somitogenesis and segmentation, along with numerous other excellent developmental biology talks. Tatsuo Fukagawa showed how the Z centromere could be deleted in DT40 cells and replaced with an engineered constitutive centromere or by selective   neocentromere evolution at a variety of locations along Z. Andrew Sinclair and Mike Clinton described the latest developments in chicken gonadal and cell autonomous somatic sex determination, respectively. Dave Burt discussed the soon-to-appear duck genome sequence and noted that reports collected at the meeting suggest that there are now at least 54 unique avian genome projects underway. Several excellent student talks and posters were also presented. The 7^th International meeting (soon to get a new, more pan-avian inclusive name) is to be held in Nagoya, Japan in November, 2012, and preliminary plans are underway for the 8^th meeting at Caltech (Pasadena, California) in 2014.'