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Series GSE104924 Query DataSets for GSE104924
Status Public on Jan 14, 2019
Title Impact of depeltion of CG5694/ova on transcription in Drosophila ovaries [miRNA- and RNA-seq]
Organism Drosophila melanogaster
Experiment type Expression profiling by high throughput sequencing
Non-coding RNA profiling by high throughput sequencing
Summary Purpose: To analysis Ova impact on transcription in Drosophila ovaries by mRNA-seq and small RNA-seq
Methods: mRNA-seq and small RNA-seq of RNA extracted from Drosophila ovaries
Results: Ova has no obvious impact on protein coding genes expression or piRNA biogenesis.
 
Overall design Isolation of total mRNA from w1118(Ctrl) and germline-specific nosGAL4 driven ova RNAi ovaries, followed by deep sequencing analysis. Purification of total RNA from w1118(Ctrl) and germline-specific nosGAL4 driven ova RNAi ovaries using PEG8000 protocol.
We extracted the small RNA according to proper size ( Seperation of 18-30 nt small RNA according to appropriate RNA markers), followed deep sequencing. We normalized the total reads number of small RNA from w1118(ctrl) and ova RNAi samples. After filtering the tRNA,  snRNA, and miRNA, we got the small RNAs mapping to the repeat regions in Drosophila genome. For wild-type, it is usually a small peak at 21 nt representing endo-siRNAs and the rest peaks at 25 nt represented piRNAs. As it remains essentially unchanged in both w1118 and ova RNAi samples for both small RNA size distribution and abandunce (data provided in the smallRNA.txt), we conclude that Ova is not required for piRNA biogenesis.
 
Contributor(s) Yang F, Xi R
Citation missing Has this study been published? Please login to update or notify GEO.
Submission date Oct 13, 2017
Last update date May 15, 2019
Contact name huanwei huang
E-mail(s) hhw2436@gmail.com
Organization name NIBS
Street address 7 Science Park Rd., ZGC life science park
City Beijing
ZIP/Postal code 102206
Country China
 
Platforms (2)
GPL9061 Illumina Genome Analyzer II (Drosophila melanogaster)
GPL17275 Illumina HiSeq 2500 (Drosophila melanogaster)
Samples (12)
GSM2810094 w1118_1
GSM2810095 w1118_2
GSM2810096 w1118_3
This SubSeries is part of SuperSeries:
GSE104925 Impact of CG5694/ova in Drosophila ovaries
Relations
BioProject PRJNA414175
SRA SRP119897

Download family Format
SOFT formatted family file(s) SOFTHelp
MINiML formatted family file(s) MINiMLHelp
Series Matrix File(s) TXTHelp

Supplementary file Size Download File type/resource
GSE104924_dLsd1RNAi_TE_Counts.txt.gz 1.4 Kb (ftp)(http) TXT
GSE104924_ova_w.TE.expression.txt.gz 3.3 Kb (ftp)(http) TXT
GSE104924_smallRNA.txt.gz 330 b (ftp)(http) TXT
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Raw data are available in SRA
Processed data are available on Series record

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