population-transcriptomics / pseudo-random-primers Goto Github PK

Figure: Pseudo-random primers can be used to reduce the amount of reads matching rRNA in transcriptome libraries (left panel), without impairing gene detection (right panel). Replicate experiments performed on total RNA extracted from HeLa or THP-1 cell cultures. The reverse transcription primers types were: Random (all 4096): the standard mixture of 4096 different hexamers; Pseudo-random (40): 40 pseudo-random selected for their distance with rRNA sequences; and Random (only 40): 40 hexamers selected completely randomly.

This repository contains supplemental files related to our manuscript published in BioTechniques:

Targeted reduction of highly abundant transcripts using pseudo-random primers. Ophélie Arnaud, Sachi Kato, Stéphane Poulain and Charles Plessy. Biotechniques. 2016 Apr 1;60(4):169-74. doi:10.2144/000114400. PMID:27071605.

The repository only contains light files. In particular FASTQ and BAM files are available for download at http://genome.gsc.riken.jp/plessy-20160322/plessy-20160322.tar.gz, or from Zenodo [FASTQ] [BAM].

The branch "BioTechniques-2016" contains the supplemental data in its state at the time of publication, but in the master branch, the files have evolved for better formatting, or following questions from readers, or following the needs to produce new figures for presentations.

This was supplemental file 1 in the manuscript [Notebook] [R source].

This includes contents from supplemental files 2 and 3. [Notebook] [R source]

This includes contents from supplemental files 2 and 4. [Notebook] [R source]

This includes contents from supplemental files 2 and 5. [Notebook] [R source]

This includes contents from supplemental files 2 and 6. [Notebook] [R source]

This was supplemental file 7. [HTML] [R source]

This was supplemental file 8. [Notebook] [R source]