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| Status |
Public on Apr 05, 2016 |
| Title |
s2_Hrp48-TRIBE_Nascent_rep1 17 |
| Sample type |
SRA |
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| Source name |
s2 cell
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| Organism |
Drosophila melanogaster |
| Characteristics |
cell type: s2 cell
tribe protein expression: induced
rna: nascent RNA
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| Extracted molecule |
total RNA |
| 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)
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| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 2000 |
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| Description |
nuclear RNA
Nascent RNA was extracted from S2 cells, according to Khodor et al. (2011) and depleted of ribosomal RNA according to Pennington et al. (2013) and mRNA (two rounds of pA depletion using Invitrogen Dynabeads Oligo dT, according to manufacturer’s protocol).
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| 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
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| Submission date |
Feb 18, 2016 |
| Last update date |
May 15, 2019 |
| Contact name |
Aoife McMahon |
| E-mail(s) |
[email protected], [email protected]
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| Organization name |
Brandeis University
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| Department |
Biology
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| Lab |
Michael Rosbash ([email protected])
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| Street address |
415 South St
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| City |
Waltham |
| State/province |
Massachusetts |
| ZIP/Postal code |
02454 |
| Country |
USA |
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| Platform ID |
GPL13304 |
| Series (1) |
| GSE78065 |
TRIBE : Hijacking an RNA-editing enzyme to identify cell-specific targets of RNA-binding proteins |
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| Relations |
| Reanalyzed by |
GSM3278712 |
| SRA |
SRX1592047 |
| BioSample |
SAMN04503038 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSM2065924_rnaedit_AMLib06_2_AG2.txt.threshold.threshold.bedgraph.gz |
61.4 Kb |
(ftp)(http) |
BEDGRAPH |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data provided as supplementary file |
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