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Status |
Public on Jun 15, 2020 |
Title |
Rrp40-G11A |
Sample type |
SRA |
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Source name |
Head Tissue
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Organism |
Drosophila melanogaster |
Characteristics |
fly strain: w1118 tissue: Head tissue age: Day 0 genotype: Rrp40-G11A/Rrp40-G11A
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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
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Library strategy |
RNA-Seq |
Library source |
transcriptomic |
Library selection |
cDNA |
Instrument model |
Illumina Genome Analyzer |
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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
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Submission date |
Mar 16, 2020 |
Last update date |
Jun 15, 2020 |
Contact name |
Derrick Jerone Morton |
E-mail(s) |
djmorto@emory.edu
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Phone |
7702899986
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Organization name |
Emory
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Department |
Biology
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Lab |
Corbett
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Street address |
1510 Clifton Rd NE
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City |
Atlanta |
State/province |
GA |
ZIP/Postal code |
30084 |
Country |
USA |
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Platform ID |
GPL9058 |
Series (1) |
GSE147032 |
A Drosophila Model of Pontocerebellar Hypoplasia Reveals a Critical Role for the RNA Exosome in Neurons |
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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 Selector |
Raw data are available in SRA |
Processed data provided as supplementary file |
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