Targeted reduction of highly abundant transcripts with pseudo-random primers
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NC17_clean
NC22b_clean
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PseudoRandomPrimers.png
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README.md
pseudo-random-primers.Rproj

README.md

Targeted reduction of highly abundant transcripts with pseudo-random primers

Pseudo-random primers

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.

Scripts and programs used in the data analysis:

Selection of the pseudo-random primers.

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

Analysis of the first experiment, NCms10058.

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

Analysis of the second experiment, NC12.

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

Analysis of the third experiment, NC17.

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

Common analysis of the three experiments.

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

Statistical analysis.

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

Analysis of the fourth experiment regarding the RNA extracted from blood, NC22.

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