|
| Status |
Public on Jan 25, 2013 |
| Title |
ChREBP fat body knockdown, wandering L3 FB_control diet-reared_biological rep 1 |
| Sample type |
SRA |
| |
|
| Source name |
ChREBP fat body knockdown, wandering L3 FB_control diet-reared
|
| Organism |
Drosophila melanogaster |
| Characteristics |
tissue: fat body
developmental stage: wandering third instar larva
Sex: female
genotype/variation: Mio/dMondo/dChREBP mutant
diet: control diet
|
| Treatment protocol |
Animals were reared on control or high sucrose Semi-Defined food from embryo hatch until harvest as wandering L3. Fat bodies were isolated, placed into Tripure, and frozen.
|
| Growth protocol |
Animals were reared at 25C on Bloomington Semi-Defined Food with sucrose substituted for glucose (0.15M). High sugar food contained 0.7M sucrose instead of 0.15M.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Tripure extraction of total RNA was performed according to the manufacturer's instructions; RNA was DNase-treated and then cleaned on a Qiagen RNeasy column and eluted in RNase-free H2O.
Bar-coded cDNA were prepared from 10 ug total RNA according to a published protocol (Haynes et al, PLoS Pathog 7, e1002411, 2011). 0.15_wt_1 was bar coded with ATCT. 0.15_wt_2:ATCT. 0.15_wt_3:ATCT. 0.15_wt_4:CCAT. 0.15_wt_5:GTGT. 0.15_wt_6:AATT.0.15_wt_1 was bar coded with ATCT. 0.15_wt_2:ATCT. 0.15_wt_3:ATCT. 0.15_wt_4:CCAT. 0.15_wt_5:GTGT. 0.15_wt_6:AATT. 0.15_chr_1: CACT. 0.15_chr_2:CACT. 0.15_chr_3:CACT. 0.7_wt_1: GGTT. 0.7_wt_2: GGTT. 0.7_wt_3:GGTT. 0.7_wt_4:TGCT. 0.7_wt_5:CGGT. 0.7_wt_6:GAAT. 0.7_chr_1:TAGT. 0.7_chr_2: TAGT
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina Genome Analyzer IIx |
| |
|
| Description |
Mio/dMondo/dChREBP mutant tissue
|
| Data processing |
To produce bed alignments, sequenced reads were aligned to the D. melanogaster UCSC dm3 assembly using Tophat (v1.3.2) and Bowtie (v0.12.7). Default Tophat settings were used.
Gene expression was quantified by processing the Tophat produced bam alignments with Cufflinks (v1.1.0) and the modENCODE MB8 annotation.
Expression was normalized by applying upper-quartile normalization as defined in "Evaluation of statistical methods for normalization and differential expression in mRNA-Seq experiments", Bullard et al. BMC Bioinformatics. 2010; 11: 94
Genome_build: MB8
Supplementary_files_format_and_content: Excel worksheet "Matrix" containing normalized RPKM for each raw dataset, indexed by CG (gene)
|
| |
|
| Submission date |
Jan 24, 2013 |
| Last update date |
May 15, 2019 |
| Contact name |
Thomas John Baranski |
| E-mail(s) |
[email protected]
|
| Organization name |
Washington University School of Medicine
|
| Street address |
660 S. Euclid Ave. Box 8127
|
| City |
Saint Louis |
| State/province |
MO |
| ZIP/Postal code |
63110 |
| Country |
USA |
| |
|
| Platform ID |
GPL11203 |
| Series (1) |
| GSE43734 |
Expression data from 0.15M and 0.7M-fed wild-type and ChREBP mutant, third instar Drosophila larval fat bodies (FBs) |
|
| Relations |
| Reanalyzed by |
GSM3282058 |
| SRA |
SRX219322 |
| BioSample |
SAMN01901736 |
