Tag Archives: Transcriptome sequencing

Transcriptome Sequencing In Translational Oncology Research

By using novel microfluidic tools, a team of researchers at Indiana University School of Medicine uncovered an unexpected ability of cancer cells to navigate and exit microscopic mazes along the shortest path. To explain this behavior, they propose a novel mechanism that guides cancer cell migration.

Find out how they have harnessed RNA-seq on tumor tissues to reveal efficacious drug targets and implement rational drug combinations in triple-negative breast cancer. Further, ongoing work on how RNA-seq is being used for biomarker discovery in retrospective cancer clinical trials will also be presented.

1,000 Fish Transcriptome Project

The China National Genebank (CNGB) announces the official launch of the 1,000 Fish Transcriptome Project (Fish T1K). It marks the beginning of an amazing transcriptome study designed to unveil the mysteries of the origin, evolution, and diversification of the largest group of vertebrates.

The findings could enable scientists to pursue innovative approaches and strategies to address challenges in fish breeding, disease control and prevention, seafood safety and biodiversity conservation.

Read more at BGI news

De Novo Transcriptome of a Model Organism to Study Tissue Regeneration

Newts have an extraordinary ability to regenerate tissues. For example, they can re-grow fully functional limbs after amputation. In addition, regeneration of parts of the central nervous system, the heart, and the lens has been characterized, making them an excellent model organism for studying regenerative processes. However, because of their enormous genome size (10 times that of human), the molecular mechanisms behind this amazing regenerative process are largely unknown.

A research group at the Max Plank Institute recently published a de novo assembly of the transcriptome of the urodelian amphibian Notophthalmus viridescens (Looso M. et al. ). The researchers combined 454, Illumina, and Sanger sequencing data from both normalized and non-normalized cDNA libraries. The resulted transcriptome comprises over 120,000 non-redundant transcripts. Homology search using BLAST led to annotation of 38,000 transcripts. Importantly, they found 800 transcripts, whose protein-coding potential was validated by mass spectrometry, that show no similarity to any know transcripts or show similarity to urodele-specific EST sequences. Some of these transcripts belong to novel protein families.

It is an interesting hypothesis that some of those newt-specific proteins may provide mechanistic insights into regeneration processes unique to these animals. Their work will definitely be an important resource for subsequent studies in tissue regeneration and may benefit future research in regenerative medicine.

NGS Favourites – Launch

Dear Blog readers,
today I am really delighted to announce the launch of the NGS Favourites.

NGS Favourites are the straightforward solution for your Next Generation Sequencing project. They are based on the wealth of knowledge that we have accumulated from over 5 years of servicing the NGS community and represent optimised packages for common NGS applications.

The NGS Favourites stand out due to:

  • Project-oriented solutions
  • Economic costs
  • Easy ordering

The NGS Favourites are available for different fields of applications:

  • Genome Sequencing Favourites - using shotgun (SG) libraries only or a combination of SG and LPE libraries
  • Transcriptome Sequencing Favourites – receive comprehensive data you can really build on
  • Exome Sequencing Favourites – sequence 6 human Exomes with the Illumina TruSeq Kit
  • Library Service Favourites – get your libraries for GS FLX sequencing prepared from us

Find your suitable Favourite and explore the easy way of sequencing with us as your professional project partner.

Winter Special: Transcriptome sequencing on Illumina HiSeq 2000

As a NGS Winter Special we do offer you a selection of our well-proven portfolio for transcriptome sequencing. De novo sequencing of eukaryotic transcriptomes will provide you a deep insight into the transcriptome without the need for a reference sequence. With the expression profiling package you will gain high resolution information about expression levels of your bacterial genes.

 

De novo sequencing of 4 or 8 eukaryotic transcriptomes using Illumina HiSeq 2000

4x or 8x Illumina cDNA library (mRNA-Seq protocol)

Sequencing in 1 channel with 2x 100 bp paired end module

4x or 8x de novo assembly of data

Special price: starting from 1,490 € / RNA sample

Expression profiling of 12 bacterial transcriptomes on Illumina HiSeq 2000

12x Illumina cDNA library with rRNA depletion

Sequencing in 1 channel with 1x 100 bp single read module

12x mapping of reads against reference genome, read counting & SNP calling

Special price: 990 € / RNA sample

 

All Services include library generation, data analysis & data delivery. The Winter Special is valid until 31.12.2011

Read more about our NGS Winter Special >