|
| Status |
Public on May 30, 2022 |
| Title |
mef2>NUAK550 whole replicate 2 |
| Sample type |
SRA |
| |
|
| Source name |
L3 whole larvae
|
| Organism |
Drosophila melanogaster |
| Characteristics |
tissue: L3 whole larvae
genotype: NUAK OE
|
| Growth protocol |
Flies were maintained on standard cornmeal-yeast-agar medium at 25 °C
|
| Extracted molecule |
total RNA |
| Extraction protocol |
RNA was harvested using Rneasy mini plus kit (Qiagen). 2.0 ug of total RNA was used for the construction of sequencing libraries.
Libraries for RNA-seq were prepared using NEBNext Ultra II RNA Library Prep Kit following manufacturer's protocols.
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 4000 |
| |
|
| Description |
matrix column name: NUAK550_whole_2
|
| Data processing |
Sequence reads were trimmed for adaptor sequence/low-quality sequence using Trimmomatic v.0.36
Trimmed sequence reads were mapped using the STAR aligner v.2.5.2b
Unique gene hit counts were calculated using featureCounts from the Subread package v.1.5.2
Differential gene expression was determined using DESeq2 and significance was defined as p-values of <0.05.
Assembly: Drosophila melanogaster BDGP6 reference genome
Supplementary files format and content: Individual .txt files of unique gene hit counts. Only unique reads that fell within exon regions were counted. If a strand-specific library preparation was performed, the reads were strand-specifically counted.
|
| |
|
| Submission date |
May 26, 2022 |
| Last update date |
May 30, 2022 |
| Contact name |
Erika R Geisbrecht |
| E-mail(s) |
geisbrechte@ksu.edu
|
| Phone |
785-532-3105
|
| Organization name |
Kansas State University
|
| Department |
Biochemistry and Molecular Biophysics
|
| Street address |
141 Chalmers Hall, Chalmers Hall
|
| City |
Manhattan |
| State/province |
KS |
| ZIP/Postal code |
66506-8008 |
| Country |
USA |
| |
|
| Platform ID |
GPL21306 |
| Series (1) |
| GSE204894 |
Gene expression profiling of NUAK kinase overexpression in Drosophila larval muscle development |
|
| Relations |
| BioSample |
SAMN28680948 |
| SRA |
SRX15471276 |
