|
| Status |
Public on Sep 30, 2015 |
| Title |
sug LSD 1.5h repB |
| Sample type |
SRA |
| |
|
| Source name |
sugarbabe null mutant (sug17d/sug def) 3rd instar control diet
|
| Organism |
Drosophila melanogaster |
| Characteristics |
genotype: sug17delta/Df(2R)Exel7123
tissue: whole larvae
developmental stage: 3rd instar
|
| Growth protocol |
Control and sugarbabe knockdown flies were kept in egg laying champers with apple juice plates and yeast paste for 3 hours. 24 hours later the 1st instar larvae were transferred to 10% yeast plates. 24 hours later larvae were transferred to either a 10% yeast + 20% sucrose or a fresh 10% yeast plate. Non-feeding larvae were removed after 1.5 hours. Low sugar samples were collected at the 1.5h time point and high sugar samples were collected 8 hours after the transfer.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Larvae were frozen in liquid nitrogen and homogenized with a disposable plastic pestle in lysis buffer and vortexed. Samples were frozen for complete lysis of the tissue. Total RNA was extracted with Nucleospin RNA II kit according to manufacturer's protocol. Elution was done with water and the samples stored at -80°C.
Library contruction was done using standard Illumina stranded mRNA protocol.
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina NextSeq 500 |
| |
|
| Data processing |
Alignment to reference genome was done with BWA v.0.5.9 with default parameters.
Reads with MAPQ >= 10 were selected to further processing with Samtools.
Exon level read counts were processed with HTSeq 0.6.1 using MAPQ >= 10 reads.
Genome_build: FlyBase Drosophila melanogaster r5.54
Supplementary_files_format_and_content: Tab-delimined txt file contains read exon counts for each sample
|
| |
|
| Submission date |
Jul 15, 2015 |
| Last update date |
May 15, 2019 |
| Contact name |
Ville Hietakangas |
| E-mail(s) |
[email protected]
|
| Organization name |
University of Helsinki
|
| Street address |
Viikinkaari 9
|
| City |
Helsinki |
| ZIP/Postal code |
00790 |
| Country |
Finland |
| |
|
| Platform ID |
GPL19132 |
| Series (2) |
| GSE70979 |
Sugar responsive regulatory network that controls organismal carbohydrate, amino acid and lipid homeostasis [set 2] |
| GSE70980 |
Sugar responsive regulatory network that controls organismal carbohydrate, amino acid and lipid homeostasis |
|
| Relations |
| Reanalyzed by |
GSM3275995 |
| BioSample |
SAMN03862104 |
| SRA |
SRX1098302 |
