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Sample GSM4412821 Query DataSets for GSM4412821
Status Public on Jun 15, 2020
Title Rrp40-G11A
Sample type SRA
 
Source name Head Tissue
Organism Drosophila melanogaster
Characteristics fly strain: w1118
tissue: Head tissue
age: Day 0
genotype: Rrp40-G11A/Rrp40-G11A
Extracted molecule total RNA
Extraction protocol Adult fly heads were removed, flash frozen on dry ice, and RNA was harvested using Trizol reagent. Illumina TruSeq RNA Sample Prep Kit was used with 1 ug of total RNA for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using standard Illumina protocols
 
Library strategy RNA-Seq
Library source transcriptomic
Library selection cDNA
Instrument model Illumina Genome Analyzer
 
Data processing The reads were mapped to the BDGP D. melanogaster (r6.25) genome. Several sequence datasets were downloaded from GenBank and FlyBase for initial assessment of the data including: 1) All Drosophila ribosomal sequences found in Genbank: Drosophila_rRNA.fa; 2) All FlyBase D. melanogaster transcripts from assembly r6.25: dmel_transcripts_r6.25.fa. Adapters were trimmed from raw reads using Trimmomatic (ver. 0.36), and trimmed reads were aligned to the ribosomal sequences using Bowtie2, and only reads which did not map to the ribosome were kept for downstream analysis.
Non-ribosomal reads were then mapped to D. melanogaster r6.25 using Tophat2. The resulting aligned reads were compared using DESeq2
 
Submission date Mar 16, 2020
Last update date Jun 15, 2020
Contact name Derrick Jerone Morton
E-mail(s) djmorto@emory.edu
Phone 7702899986
Organization name Emory
Department Biology
Lab Corbett
Street address 1510 Clifton Rd NE
City Atlanta
State/province GA
ZIP/Postal code 30084
Country USA
 
Platform ID GPL9058
Series (1)
GSE147032 A Drosophila Model of Pontocerebellar Hypoplasia Reveals a Critical Role for the RNA Exosome in Neurons
Relations
BioSample SAMN14382606
SRA SRX7915300

Supplementary file Size Download File type/resource
GSM4412821_G11AR.pooled.UM.sorted.bw 62.0 Mb (ftp)(http) BW
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file

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