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Sample GSM2065948

Query DataSets for GSM2065948

Status

Public on Apr 05, 2016

Title

s2_gDNA 41

Sample type

SRA

Source name

s2 cell

Organism

Drosophila melanogaster

Characteristics

cell type: s2 cell
tribe protein expression: N/A

Extracted molecule

genomic DNA

Extraction protocol

s2 cell mRNA libraries were prepared using Illumina Truseq kits according to manufacturers protocol. S2 cell nascent RNA libraries were prepared according to Khodor et al. (2011). Neuronal cell sorting libraries were prepared according to Abruzzi et al, 2015. CLIP libraries were prepared according to Cho et al., 2012)

Library strategy

OTHER

Library source

genomic

Library selection

other

Instrument model

Illumina HiSeq 2000

Description

control

Data processing

Basecalls performed using CASAVA version 1.7
RNA editing analysis is performed as described in Rodriguez et al, 2012, with some modifications.
In brief, sequencing reads are trimmed with Trimmomatics (Bolger et al., 2014) by 6bp at each end, additional low quality bases from either end are removed and reads with average quality score of 30 or greater are kept. Reads were aligned to the Drosophila genome (Release 5/dm3) using Genomic DNA reads are aligned using bowtie2 (parameters: --sensitive) to the reference genome (Release 5/dm3) and RNA sequencing reads are aligned using tophat2 (Trapnell et al., 2009) (parameters: -m 1 -p 5 -g 2 -I 50000 --microexon-search --no-coverage-search). Only events with minimum 20 reads and 10% editing were considered to be an editing events. Code for RNA editing analysis is available here: https://github.com/rosbashlab/TRIBE
The gtf file used throughout the analysis was downloaded from iGenomes (via Illumina, dm3 build). The editing analysis pipeline used RefSeq annotation of genes, which were downloaded from UCSC genome browser.
CLIP sequence reads were aligned using Novoalign, (novoalign -t 85 -l 23 -s 1 -r None). Subsequent bioinformatic analysis of CLIP data was performed as described in Moore et al. (2014) and using the CLIPper algorithm (available at https://github.com/YeoLab/clipper) with default settings.
Genome_build: Release 5/dm3
Supplementary_files_format_and_content: RNA editing sites are provided in bedgraph file format, (Chromosome, co-ordinate, co-ordinate, edit %, edit%_number of total reads). CLIP

Submission date

Feb 18, 2016

Last update date

May 15, 2019

Contact name

Aoife McMahon

E-mail(s)

mcmahona@brandeis.edu, reazur@brandeis.edu

Organization name

Brandeis University

Department

Biology