|
| Status |
Public on Aug 08, 2018 |
| Title |
Dvpdf_con_REP1_expressions |
| Sample type |
SRA |
| |
|
| Source name |
brains
|
| Organism |
Drosophila melanogaster |
| Characteristics |
cell type: dvpdf neurons
rna: mRNA
sample type: control
|
| Treatment protocol |
nonA is downregulated by RNA interference in dvpdf cells in fly brains
|
| Extracted molecule |
total RNA |
| Extraction protocol |
mRNAs extraction and amplification were prepared according to Nagoshi 2010 et al and Abruzzi et al 2016
Libraries were prepared using using illumina Truseq kits
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 2000 |
| |
|
| Data processing |
RNA sequencing data were analyzed as described in (Rodriguez et al., 2012; McMahon et al., 2016)
Scripts available on GitHub (https://github.com/rosbashlab/).
Alignment to dm3 genome was done with Tophat v2.1.1 with referenence annotation in gtf format. Multimapped reads are removed. Expression levels were quantified by cufflinks (Trapnell et al., 2012).
Genome_build: Release 5/dm3
Supplementary_files_format_and_content: RNA editing sites are provided in bedgraph file format
|
| |
|
| Submission date |
Jun 28, 2018 |
| Last update date |
Aug 08, 2018 |
| Contact name |
weifei luo |
| E-mail(s) |
wluo@brandeis.edu
|
| Phone |
781-736-3163
|
| Organization name |
Brandeis University
|
| Department |
Department of Biology
|
| Lab |
Rosbash
|
| Street address |
415 South st
|
| City |
waltham |
| State/province |
MA |
| ZIP/Postal code |
02454 |
| Country |
USA |
| |
|
| Platform ID |
GPL13304 |
| Series (1) |
| GSE116408 |
Gene expression of NonA RNAi knockdown in dvpdf cells in Drosophila |
|
| Relations |
| BioSample |
SAMN09515178 |
| SRA |
SRX4321103 |
