|
| Status |
Public on Oct 25, 2020 |
| Title |
A2: Control (w[1118]; Gpdh1[12]/+) |
| Sample type |
SRA |
| |
|
| Source name |
mid-L3 larvae
|
| Organism |
Drosophila melanogaster |
| Characteristics |
genotype: Control (w[1118]; Gpdh1[12]/+)
tissue: mid-L3 larvae
|
| Growth protocol |
Drosophila eggs were collected on molasses egg caps with yeast paste an maintained at 25ºC for 60 hours.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Larvae were collected as described in Li, H., Tennessen, J. M. Preparation of Drosophila Larval Samples for Gas Chromatography-Mass Spectrometry (GC-MS)-based Metabolomics. J. Vis. Exp. (136), e57847, doi:10.3791/57847 (2018). RNA was extracted using a Qiagen RNeasy Mini Kit.
RNA libraries were prepared for sequencing using standard Illumina protocols
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina NextSeq 500 |
| |
|
| Data processing |
Samples were demultiplexed with bcl2fastq v2.20.0.422
Adapters and low quality sequences were removed with cutadapt v1.12 using the options "-m 30 -q 30"
Read with fewer than 30 high quality bases were excluded from further analysis
Reads were mapped against dmel r6.21 using hisat2 version 2.1.0 with the parameters "--no-unal"
Mapped reads were assigned to genes using the FlyBase dmel annotation 6.21 with htseq-count 0.9.0
Genome_build: dmel r6.21
Supplementary_files_format_and_content: tab-delimited text files including gene counts for each sample
|
| |
|
| Submission date |
Oct 26, 2018 |
| Last update date |
Oct 26, 2020 |
| Contact name |
Jason Tennessen |
| E-mail(s) |
[email protected]
|
| Phone |
812 855 9803
|
| Organization name |
Indiana University
|
| Department |
Department of Biology
|
| Street address |
1001 E. Third St
|
| City |
Bloomington |
| State/province |
IN |
| ZIP/Postal code |
47405 |
| Country |
USA |
| |
|
| Platform ID |
GPL19132 |
| Series (1) |
| GSE121876 |
RNAseq analysis comparing gene expression in Drosophila Gpdh1 mutant and Gpdh1; Ldh double mutants vs control strains |
|
| Relations |
| BioSample |
SAMN10330869 |
| SRA |
SRX4941275 |
