|
| Status |
Public on Jun 30, 2016 |
| Title |
RNA-seq from Piwi-KD |
| Sample type |
SRA |
| |
|
| Source name |
Piwi-KD OSC
|
| Organism |
Drosophila melanogaster |
| Characteristics |
cell type: Ovarian Somatic Cells (OSC)
variation: RNAi Piwi
|
| Treatment protocol |
Transfection of siRNAs was performed using Cell Line 96-well Nucleofector Kit SF and 96-well Shuttle Device (Lonza).
|
| Growth protocol |
Cells were grown at 26 degrees on OSC medium (Fly Extract added M3 medium).
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNAs were isolated with the Isogen reagent (NipponGene). Poly(A)+ RNAs were obtained using Oligo-dT beads.
Poly(A)+ RNA libraries were prepared as described (Ohtani et al., 2013).
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 2500 |
| |
|
| Description |
processed_RNAseq.txt
|
| Data processing |
RNA-seq analysis was performed as previously described (Ohtani et al., 2013) with slight modifications. Briefly, Cutadapt was used to remove adapter sequences from RNA-seq reads. Reads shorter than 20 nt were removed. Bowtie 2.0.6 (Langmead and Salzberg, 2012) was used with default parameters to map sequences to the Drosophila genome (dm3). Reads mapped to the genome were then mapped to the Drosophila melanogaster transposon consensus sequence from Repbase (Jurka, 1998), extracting those that were uniquely mapped. Expression levels (RPKM) of transposons were calculated using transposon consensus sequence mapped reads. Expression levels (RPKM) of Pol II-regulated genes were calculated using TopHat 2.0.7 (Trapnell et al., 2009) and cufflinks 2.1.1. (Trapnell et al., 2010).
Genome_build: dm3
Supplementary_files_format_and_content: Normalized read counts mapped to each transposon consensus sequence (Tab delimited format, txt).
|
| |
|
| Submission date |
May 13, 2016 |
| Last update date |
Jul 03, 2021 |
| Contact name |
Yuka W. Iwasaki |
| E-mail(s) |
iwasaki@keio.jp
|
| Organization name |
Keio University School of Medicine
|
| Department |
Department of Molecular Biology
|
| Lab |
Siomi Lab
|
| Street address |
35 Shinanomachi, Shinjuku-ku,
|
| City |
Tokyo |
| ZIP/Postal code |
160-8582 |
| Country |
Japan |
| |
|
| Platform ID |
GPL17275 |
| Series (1) |
| GSE81434 |
Piwi modulates chromatin accessibility by regulating multiple factors including histone H1 to repress transposons |
|
| Relations |
| Reanalyzed by |
GSM3281176 |
| BioSample |
SAMN04999486 |
| SRA |
SRX1760692 |
