|
| Status |
Public on Mar 10, 2020 |
| Title |
Myb mutant sample 3 [M3] |
| Sample type |
SRA |
| |
|
| Source name |
Wing discs of Myb mutant 3rd instar larvae
|
| Organism |
Drosophila melanogaster |
| Characteristics |
genotype/variation: Myb^MH107: mutation induced by P-element mobilization by Delta2-3 transposase
phenotype: Lethal-early pupal stage
Sex: male
developmental stage: 3rd instar larvae
tissue: wing discs
|
| Treatment protocol |
3rd instar larvae were dissected in 1X PBS (pH 7.4)
|
| Growth protocol |
Flies were mantined at 25°C in malt-based media (Archon Scientific).
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA was isolated from yw67 control (3 biological replicates) and Myb mutant (5 biological replicates) 3rd instar mesothoracic wing discs and cDNA was generated from polyadenylated mRNA captured with oligo-dT beads. The cDNA was then sequenced on two lanes (all 8 samples) of anIllumina HiSeq 4000 (Iowa Institute of Human Genetics).
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 4000 |
| |
|
| Description |
Myb mutant imaginal wing discs of 3rd instar larvae. Second technical replicate of the third biological replicate
|
| Data processing |
Conventional base calling was performed using Sanger/Illumina 1.9 encoding.
Sequenced reads were trimmed for adaptor sequence using Trimmomatic-0.22. An average quality of 20 was maintained for all sequences. Aberrant bases (15 bp from the start and bases after 125bp) were trimmed of each sequence based on fastqc analysis . Trimmed sequences between 36bp and 125bp were retained for further analysis. Reads from the two lanes were then combined to generate one alignment file for each of the 8 samples using bowtie. Reads were mapped to dmel r5.7 gene exons using bowtie2-2.1.0 with default parameters.
The eXpress tool was used to generate uniquely mapped read counts for each exon of a gene. The sum of unique read counts for each gene was generated using a custom python script. The DESeq2 package in R was used to compute normalized fold-change and P value for each gene, comparing Myb mutant to control.
Genome_build: dmel r5.7
Supplementary_files_format_and_content: The processed data file is a tab delimited file that contains flybase id, associated refSeq gene symbol, read counts for each gene per sample and additional data generated using DESeq2 package in R such as log2 fold change (mutant/control), p-value and adj p-value.
|
| |
|
| Submission date |
Oct 03, 2019 |
| Last update date |
Mar 10, 2020 |
| Contact name |
David H Price |
| E-mail(s) |
david-price@uiowa.edu
|
| Organization name |
University of Iowa
|
| Department |
Biochemistry and Molecular Biology
|
| Lab |
260 EMRB
|
| Street address |
500 Newton Road
|
| City |
Iowa City |
| State/province |
IA |
| ZIP/Postal code |
52242 |
| Country |
USA |
| |
|
| Platform ID |
GPL21306 |
| Series (2) |
| GSE100143 |
Drosophila melangoaster Myb mutant wing discs of 3rd instar larvae. |
| GSE138373 |
RNA-seq expression analysis of control and Myb mutant wing discs |
|
| Relations |
| BioSample |
SAMN12906217 |
