Selected article for: "bat genome and data set"
Author: Nelly Mostajo Berrospi; Marie Lataretu; Sebastian Krautwurst; Florian Mock; Daniel Desirò; Kevin Lamkiewicz; Maximilian Collatz; Andreas Schoen; Friedemann Weber; Manja Marz; Martin Hölzer
Title: A comprehensive annotation and differential expression analysis of short and long non-coding RNAs in 16 bat genomes
  • Document date: 2019_8_19
    • ID: ihqvcxv6_16
    Snippet: To enable a better investigation of small RNAs (sRNAs), we included a data set of the targeted sequencing of sRNAs (especially miRNAs) from M. daubentonii cells (Weber-2019). To obtain this sRNA sequencing data, total RNA of 18 samples, that was obtained using the same procedure like explained for the rRNA-depleted M. daubentonii data 36 , was preprocessed using the Illumina TruSeq smallRNA protocol, sequenced on one HiSeq 2500 lane, and finally .....
    Document: To enable a better investigation of small RNAs (sRNAs), we included a data set of the targeted sequencing of sRNAs (especially miRNAs) from M. daubentonii cells (Weber-2019). To obtain this sRNA sequencing data, total RNA of 18 samples, that was obtained using the same procedure like explained for the rRNA-depleted M. daubentonii data 36 , was preprocessed using the Illumina TruSeq smallRNA protocol, sequenced on one HiSeq 2500 lane, and finally uploaded in the course of this study under GEO accession GSE132336. The reads of these 18 sRNA samples were additionally preprocessed by removing potential adapter sequences with cutadapt 40 (v1.8.3) followed by a quality (Q20) trimming using again a window-size of 4 and a minimum length of 15 nt by PrinSeq 41 (v0.20.3). The processed sRNA samples were either individually mapped to the 16 bat genomes for differential expression analysis or combined and mapped on each bat genome to predict known and novel miRNAs with miRDeep2 42 .

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