|
| Status |
Public on Aug 01, 2023 |
| Title |
hsp70_day_23_trained_4 |
| Sample type |
SRA |
| |
|
| Source name |
legs
|
| Organism |
Drosophila melanogaster |
| Characteristics |
tissue: legs
Sex: male
treatment: training
genotype: Df(3R)Hsp70A, Df(3R)Hsp70B
age: 23 days
|
| Extracted molecule |
polyA RNA |
| Extraction protocol |
Legs from 15 flies were homogenized in the RLT buffer (Qiagen, Germany) with 1% beta-mercaptoethanol using a drill and incubated (55ºC, 10 min) with protein kinase K (Evrogen, Russia). Total RNA was extracted by a silica spin column (CleanRNA Standard, Evrogen, Russia). RNA concentration was evaluated by a fluorimetric assay (Qubit 4, Thermo Scientific). RNA integrity was evaluated in an aliquot of total RNA (200 μg) after DNase I (Thermo Scientific) treatment using capillary electrophoresis (TapeStation, Agilent, Germany).
Strand-specific libraries were prepared by the NEBNext Ultra II Directional RNA Library Preparation kit (NEB, USA)
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
NextSeq 550 |
| |
|
| Data processing |
Adapter sequences and low quality reads were trimmed using the Timmomatic tool (v0.36) (options:2:30:10 LEADING:3 TRAILING:3 SLIDINGWINDOW:4:15 MINLEN:35)
High-quality reads were aligned to the reference D. melanogaster BDGP6.94 primary genome assembly using HISAT v2.1.0
Uniqe reads were counted for known exons of each gene using Rsubread package (R) and Ensembl annotation (BDGP6.94)
TPM values calculated using kallisto v0.44.0
Assembly: BDGP6.94 primary genome assembly
Supplementary files format and content: tab-delimited text files: Read_counts.txt — uniquely aligned read counts for genes
|
| |
|
| Submission date |
Jul 27, 2023 |
| Last update date |
Aug 01, 2023 |
| Contact name |
Pavel Makhnovsky |
| E-mail(s) |
maxpauel@gmail.com
|
| Organization name |
Institute of Biomedical Problems of the Russian Academy of Sciences
|
| Lab |
Laboratory of muscle physiology
|
| Street address |
76A Khoroshevskoye shosse
|
| City |
Moscow |
| ZIP/Postal code |
123007 |
| Country |
Russia |
| |
|
| Platform ID |
GPL22106 |
| Series (1) |
| GSE239395 |
Knockout of Hsp70 genes significantly affects locomotion speed and gene expression in leg skeletal muscles of Drosophila melanogaster |
|
| Relations |
| BioSample |
SAMN36726218 |
| SRA |
SRX21170739 |
