 |
 |
GEO help: Mouse over screen elements for information. |
|
| Status |
Public on Jun 14, 2023 |
| Title |
w1118_ZT7_1_S4_ |
| Sample type |
SRA |
| |
|
| Source name |
Brain
|
| Organism |
Drosophila melanogaster |
| Characteristics |
tissue: Brain
genotype: w1118
treatment: ZT7
|
| Growth protocol |
All crosses were performed and raised at 25 °C in a 12:12 Light/Dark cycle (LD) conditions.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
RNA from the fly brains was extracted using TRIzol reagent (Sigma, T9424) and treated with DnaseI (NEB, M0303L).
150 ng of RNA as input for preparing 3' RNA sequencing libraries following CelSeq2 protocol
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina NextSeq 500 |
| |
|
| Data processing |
data were aligned to the Drosophila melanogaster dm6 genome and transcriptome version using STAR
quantification was done with ESAT
The circadian analysis was performed using the package MetaCycle
For each circadian timepoint, three replicates were analyzed. Since each replicate was sequenced separately, the counts were divided by the maximum value in each replicate after normalizing by library size. Genes with more than two zero counts at any time point were discarded. The amplitude for each replicate was calculated as the maximum divided by the minimum for each gene. The JTK algorithm was used for the circadian analysis
A gene was considered a cycler if the JTK p-adjusted value was less than 0.05 and the amplitude was more than 2.
Assembly: dm6
Supplementary files format and content: normalized counts
|
| |
|
| Submission date |
May 22, 2023 |
| Last update date |
Jun 14, 2023 |
| Contact name |
Sebastian Kadener |
| E-mail(s) |
skadener@brandeis.edu
|
| Organization name |
Brandeis University
|
| Department |
Biology department
|
| Street address |
415 South Street
|
| City |
Waltham |
| State/province |
MA |
| ZIP/Postal code |
02453 |
| Country |
USA |
| |
|
| Platform ID |
GPL19132 |
| Series (1) |
| GSE233184 |
The organismal landscape of clock cells and circadian gene expression in Drosophila |
|
| Relations |
| BioSample |
SAMN35319657 |
| SRA |
SRX20467800 |
| Supplementary data files not provided |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data are available on Series record |
|
|
|
|
 |
