Human list of RNA-seq datasets before and after hypoxic stress

List of NCBI Gene Expression Omnibus (GEO) or EBI ArrayExpress IDs before and after hypoxic stress in human. Gene expression measurement by RNA-seq

生命科学データ解析 の本を書いたので宣伝

Promotion presentation for the book, the Lectures on Biological Data Analysis by Dr. Hidemasa Bono in DBCLS (in Japanese).<div> 「Dr. Bonoの生命科学データ解析」のプロモーションプレゼンテーションです。とくに、2017年12月16日にこの本の勉強会を静岡駅前でやるので、そのお誘いです。プレビューでは日本語フォントが表示されないようなので、ダウンロードして御覧ください。</div

公共データベースを活用した生命科学研究 (Next generation research in life science making full use of publicly available databases)

<p>In order to promote life science researches, National Bioscience Database Center (NBDC) in Japan Science and Technology Agency (JST) cares for public databases in Japan. Database Center for Life Science (DBCLS) has been developing database integration technologies in tight collaboration with NBDC. In order to promote the closer cooperation with DNA Data Bank of Japan (DDBJ), some members in DBCLS geographically moved to National Institute of Genetics (NIG).<br>We are tackling the problem how to organize huge amount of nucleotide sequence data from next generation sequencers (NGS) which has been archived by DDBJ and various types of gene expression data including transcriptome sequencing data from NGS. Our mission also includes the practical application of bioinformatics approach to the cutting-edge research activities, and thus we are also collaborating with biologists who are trying to establish new types of model organisms for the study of human disease and require the development of new bioinformatics methodologies. We will introduce current status of our activity.</p

データベースを活用した知のめぐりのよい生命科学データ解析

Lecture material by Dr. Hidemasa Bono from DBCLS (in Japanese).<div>日本語フォントがプレビューで表示されないようなので、ダウンロードして中身を御覧ください。</div

知のめぐりの良い生命科学研究者の10の心得

第52回生命科学夏の学校 愛

ゲノムと遺伝子発現DBの現状ートランスオミクスのための基礎知識

jPOST Workshop 2016:プロテオームデータと生命科学データベー

Mouse microarray log ratio data before and after hypoxic stress

The expression values of the genes were calculated from the original CEL files downloaded from NCBI GEO after robust multi-array averaging (RMA) normalization by the affy package (version 1.50.0) in R (version 3.3.3)/BioConductor (version 3.3). Log-transformed (base 2) ratio of hypoxia/normoxia is described in the table

ゲノム編集におけるビッグデータ活用 (How to make use of big data in the field of genome editing)

How to make use of big data in the field of genome editing (in Japanese)

RおよびBioconductorを使ったバイオデータ解析

<p>Introduction slides for tutorial how to make use of R/Bioconductor for biological studies in Japanese.</p

Mouse list of counts after hypoxic stress (up/down/unchanged)

The number of experiments in which gene was up/down regulated was counted for all genes in mouse. For up/down regulated gene selection, over 1.5 fold threshold was adopted