|
| Status |
Public on Sep 30, 2015 |
| Title |
mlx1 LSD 1.5h repA |
| Sample type |
SRA |
| |
|
| Source name |
Mlx null mutant 3rd instar control diet
|
| Organism |
Drosophila melanogaster |
| Characteristics |
genotype: Mlx -/-
tissue: whole larvae
developmental stage: 3rd instar
|
| Growth protocol |
Control and mlx1 mutant 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 performed at BGI with the following protocol: the total RNA samples were first treated with Dnase I. Then the mRNA was enriched by using the oligo(dT) magnetic beads. Mixed with the fragmentation buffer, the mRNA was fragmented into short fragments. The first stand of cDNA was synthesized by using random hexamer-primer. Buffer, dNTPs, RNase H and DNA polymerase I were added to synthesize the second strand. The double strand cDNA was purified with magnetic beads. End reparation and 3'-end single nucleotide A addition was performed. Finally, sequencing adaptors were ligated to the fragments and fragment enrichment was done by PCR amplification.
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 2000 |
| |
|
| 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 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 |
GPL13304 |
| Series (2) |
| GSE70978 |
Sugar responsive regulatory network that controls organismal carbohydrate, amino acid and lipid homeostasis [set 1] |
| GSE70980 |
Sugar responsive regulatory network that controls organismal carbohydrate, amino acid and lipid homeostasis |
|
| Relations |
| Reanalyzed by |
GSM3275982 |
| BioSample |
SAMN03862091 |
| SRA |
SRX1098289 |
