|
| Status |
Public on Aug 01, 2013 |
| Title |
RNA-seq from Control-KD |
| Sample type |
SRA |
| |
|
| Source name |
RNAi knockdown of EGFP
|
| Organism |
Drosophila melanogaster |
| Characteristics |
cell type: Ovarian Somatic Cells (OSC)
transfected with: siRNA against EGFP (cotnrol)
|
| Treatment protocol |
OSC were transfected once with siRNAs and analyzed after 2 days
|
| 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.
The deep sequencing libraries were prepared according to TruSeq RNA Sample Prep Kit (Illumina).
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 2000 |
| |
|
| Description |
Sample 1
|
| Data processing |
Illumina Casava1.8.1 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence using cutadapt software, discarded reads shorter than 20bp, then mapped to dm3 whole genome and repbase transposable elements using bowtie2 v2.0.0 with default parameters
For calculation of Reads Per Kilobase per Million mapped reads (RPKM) of transposable elements, dm3 genome and repbase transposable element mapping result was processed using in-house perl script. In short, number of reads falling in the transposable elements were counted and normalized by the count of genome mapped reads and the length of each transposable element.
Reads Per Kilobase of exon model per Million mapped reads (RPKM) for transcripts was calculated using TopHat v2.0.7/Cufflinks v.2.0.2 with parameters -G (genes.gtf from Illumina iGenomes) --microexon_search
Genome_build: dm3 (Release 5; GCA_000001215.2)
Supplementary_files_format_and_content: tab-delimited text files include RPKM values for each transcript (*transcript.txt) and transposable elements (*TE.txt)
|
| |
|
| Submission date |
May 16, 2013 |
| 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 |
GPL13304 |
| Series (1) |
| GSE47006 |
Expression profile and RNA Polymerase II occupancy of transposable elements among knock down of the piRNA pathway components in OSCs |
|
| Relations |
| Reanalyzed by |
GSM3283341 |
| BioSample |
SAMN02146418 |
| SRA |
SRX278535 |
