|
| Status |
Public on Oct 20, 2021 |
| Title |
evening sleep deprivation ESD1 |
| Sample type |
SRA |
| |
|
| Source name |
Brain (R5 Ellipsoid Body Neurons)
|
| Organism |
Drosophila melanogaster |
| Characteristics |
tissue: Brain (R5 Ellipsoid Body Neurons)
group: evening sleep deprivation
|
| Extracted molecule |
total RNA |
| Extraction protocol |
40-45 Brains from 7-10 day old flies expressing gfp in ~15 R5 ellipsoid body neurons in morning or evening +/- sleep deprivation conditions were dissected. Flourescent-activated cell sorting (FACS) was used to isolate individual cells. Total RNA was extracted using PicoPure kit and cDNA was created using a T7-oligo-dT primer and SuperScript III and served as a template to make and amplify new mRNA using T7 RNA polymerase and the Ambion MegaScript kit .
Libraries were generated using an Illumina TruSeq Stranded Kit
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina NovaSeq 6000 |
| |
|
| Data processing |
Base calling and demultiplexing was performed with bcl2fastq.
Reads were pseudo aligned and quantified using Kallisto (v0.46.1) (Bray et al., 2016) against a prebuilt index file constructed from Ensembl reference transcriptomes (v96)
Kallisto was used to process paired end reads with 10 bootstraps.
Differential expression analysis of the resulting abundance estimate data was then performed with Sleuth (v0.30.0)
Gene-level abundance estimates were computed by summing transcripts per million (TPM) estimates for transcripts for each gene
It is abundance file which containe estimated count and TPM of the transcripts
Supplimentary data file containe Sleuth gene level differential expression results which are used for reaching the final conclusions in the manuscripts.
|
| |
|
| Submission date |
Oct 18, 2021 |
| Last update date |
Oct 20, 2021 |
| Contact name |
Ravi Allada |
| E-mail(s) |
r-allada@northwestern.edu
|
| Organization name |
Northwestern university
|
| Department |
Department of neurobiology
|
| Lab |
Allada lab
|
| Street address |
Department fo neurobiology, Noerthwestern university,, 2205 Tech Drive
|
| City |
Evanston |
| State/province |
Illinois |
| ZIP/Postal code |
60208 |
| Country |
USA |
| |
|
| Platform ID |
GPL25244 |
| Series (1) |
| GSE186076 |
Next generation sequencing of isolated R5 ellipsoid body neurons of Drosophila in the morning and evening with and without sleep deprivation |
|
| Relations |
| BioSample |
SAMN22374233 |
| SRA |
SRX12677170 |
