|
| Status |
Public on Mar 21, 2017 |
| Title |
StimKDrecovery_72h_2 |
| Sample type |
SRA |
| |
|
| Source name |
Central Nervous Sytem
|
| Organism |
Drosophila melanogaster |
| Characteristics |
time: 72h After Puparium Formation
tissue: pupal brain
dstim knockdown status: 24h knockdown + 36h recovery
genotype: ElavC155GAL4; dStimRNAi/tubulinGAL80ts
|
| Growth protocol |
Flies were reared on corn meal medium at 25°C and the temperature was raised to 29°C for knockdown
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Pupal nervous systems were disseced in PBS, immediately transferred to ice and about 10 CNS were pooled together per sample to isolate RNA using Trizol
Libraries were made with 500ng total RNA using Illumina v2 protocol with 1/3rd the kit recommended volumes. Purification and size selection using Ampure beads.
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 2000 |
| |
|
| Data processing |
Illumina Casava software used for basecalling
Good quality sequencing reads after adapter trimming were mapped to Drosophila genome using Tophat v 2.0.11 with parameters -m 1 -F 0 -p 6 -g 1 --microexon-search --no-coverage-search
Mapped reads of both conditions at each individual timepoint were used for differential expression analysis by cuffdiff v2.2.0 using default options
Gene counts for both conditions at each time point were independantly generated using BioConductor packages GenomicRanges and IRanges which were then used to call differentially expressed genes using the Bioconductor package EdgeR
Genome_build: dm3
Supplementary_files_format_and_content: tab-delimited text files with expression levels, fold change and p-values for all genes from cuffdiff and edgeR
|
| |
|
| Submission date |
Oct 25, 2016 |
| Last update date |
May 15, 2019 |
| Contact name |
Gaiti Hasan |
| E-mail(s) |
[email protected]
|
| Organization name |
NCBS, TIFR
|
| Street address |
GKVK Campus,
|
| City |
Bangalore |
| ZIP/Postal code |
560065 |
| Country |
India |
| |
|
| Platform ID |
GPL13304 |
| Series (1) |
| GSE89168 |
Transcriptomic screen to identify genes regulated by Store-operated calcium entry in Drosophila pupal nervous system |
|
| Relations |
| Reanalyzed by |
GSM3282162 |
| BioSample |
SAMN05939273 |
| SRA |
SRX2268052 |
