|
| Status |
Public on Aug 19, 2019 |
| Title |
ATF4 overexpression rep 2 |
| Sample type |
SRA |
| |
|
| Source name |
Central nervous system
|
| Organism |
Drosophila melanogaster |
| Characteristics |
developmental stage: Late third instar larvae
|
| Treatment protocol |
One control and three experimental genotypes were used: Control (nsybGal4/+), Experimental group 1: TFAM3M (nsybGal4>UAS-TFAM3M), Experimental group 2: TFAM3M, ATF4 RNAi (nsybGal4>UAS-TFAM3M, UAS-ATF4 RNAi), Experimental group 3: ATF4 overexpression (nsybGal4>UAS-ATF4-HA).
|
| Growth protocol |
Larvae were grown on standard fly food at 25 degrees celsius.
|
| Extracted molecule |
polyA RNA |
| Extraction protocol |
For each replicate, the complete CNS from 20 wandering third instar larvae were dissected in PBS and then transferred into 100ul of lysis buffer (with β-mercaptoethanol) from the Absolutely RNA Microprep kit (Stratagene) and vortexed for 5 seconds. Total RNA was then prepared using this kit. For each genotype RNA samples were prepared in quadruplicate and stored at -80 degrees celsius.
RNA samples were couriered on dry ice to the Glasgow Polyomics facility (University of Glasgow), where polyA cDNA libraries were constructed using the TruSeq Stranded mRNA Kit (Illumina).
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina NextSeq 500 |
| |
|
| Data processing |
Illumina NextSeq 500 RTA v2 used for base calling.
Adaptors were automatically trimmed from the reads by the NextSeq 500, but a check for residual untrimmed adaptors was performed by FastQC (Galaxy Version 0.52), accessed via the user interface software Galaxy (UseGalaxy.org). RNA reads were then aligned to the dm6 genome using Bowtie2 (Galaxy Version 2.3.4.2) with default settings.
Raw fragment counts were compiled by FeatureCounts (Galaxy Version 1.6.3+galaxy2), accessed via the user interface software Galaxy (UseGalaxy.org), with default settings.
Differential gene expression was assessed via DESeq2 (Galaxy Version 2.11.40.6), accessed via UseGalaxy.org, with default settings.
Genome_build: dm6
Supplementary_files_format_and_content: Excel spreadsheets containing base means, log2(fold change), fold changes, standard errors, Wald statistics, p-values and adjusted p-values for each pair of samples.
|
| |
|
| Submission date |
Aug 19, 2019 |
| Last update date |
Aug 22, 2019 |
| Contact name |
Joseph Matthew Bateman |
| E-mail(s) |
joseph_matthew.bateman@kcl.ac.uk
|
| Phone |
44-(0)207 848 8144
|
| Organization name |
King's College London
|
| Department |
Basic & Clinical Neuroscience
|
| Lab |
Maurice Wohl Clinical Neuroscience Institute
|
| Street address |
Cutcombe Road
|
| City |
London |
| ZIP/Postal code |
SE5 9RT |
| Country |
United Kingdom |
| |
|
| Platform ID |
GPL19132 |
| Series (1) |
| GSE128244 |
Drosophila CNS mitochondrial dysfunction with ATF4 inhibition RNA-Seq |
|
| Relations |
| BioSample |
SAMN12599018 |
| SRA |
SRX6733647 |
