|
| Status |
Public on Aug 01, 2016 |
| Title |
ribosomal RNA depleted total RNA from WRR-1 dsRED control knock-down cells, replicate 2 |
| Sample type |
SRA |
| |
|
| Source name |
WRR-1 cells
|
| Organism |
Drosophila melanogaster |
| Characteristics |
cell line: WRR-1 cells
treatment: dsRNA treated 5 days
genotype: w1118; Act-5C-GAL4,UAS-Wts-RNAi,UAS- RasV12 (WRR-1)
|
| Treatment protocol |
WRR-1 cells were transfected with 10ug of dsRNA against dsRED using Effectene (Qiagen); RNA was collected after 5 days.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNAs were prepared with Trizol reagent (Invitrogen).
Following ribo-zero rRNA depletion, libraries were prepared from 200ng RNAs with ScriptSeq v2 (Epicentre).
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina NextSeq 500 |
| |
|
| Description |
rRNA depleted
average insert size: ~350bp
dsREDKD_vs_control_RNAseq.xlsx
|
| Data processing |
Reads were aligned to the drosophila transcriptome using tophat2 and options -G dmel-r5.43.gff --no-novel-juncs -g 10.
Uniquely mapping reads were assigned to features (genes or genes and piRNA clusters) using HTSeq; counts matching ribosomal RNAs and transposons insertions were excluded.
Normalized counts and differential gene expression were estimated with DESeq2.
Genome_build: dm3 BDGP release 5
Supplementary_files_format_and_content: Processed files contain HTSeq counts,or DESeq2 standard processing results for knock downs compared to non transfected WRR-1 control cells; the mean of the normalized counts in replicates, and DESeq2 outputs are reported.
|
| |
|
| Submission date |
Jun 29, 2016 |
| Last update date |
May 15, 2019 |
| Contact name |
Delphine Fagegaltier |
| Organization name |
Cold Spring Harbor Lab
|
| Department |
Genomics Division
|
| Lab |
Greg Hannon
|
| Street address |
One Bungtown Rd
|
| City |
Cold Spring Harbor |
| State/province |
NY |
| ZIP/Postal code |
11724 |
| Country |
USA |
| |
|
| Platform ID |
GPL19132 |
| Series (2) |
| GSE83843 |
Characterization of active piRNAs and piRNA machinery in WRR-1 cells deficient for the Hippo pathway (deficient for the warts tumor suppressor) and expressing activated RasV12 (RNA-seq) |
| GSE83877 |
Characterization of active piRNAs and piRNA machinery in WRR-1 cells deficient for the Hippo pathway (deficient for the warts tumor suppressor) and expressing activated RasV12 |
|
| Relations |
| Reanalyzed by |
GSM3281540 |
| BioSample |
SAMN05323925 |
| SRA |
SRX1884288 |
