|
| Status |
Public on Jun 29, 2020 |
| Title |
Heads, Tau A |
| Sample type |
SRA |
| |
|
| Source name |
18 pooled Drosophila heads
|
| Organism |
Drosophila melanogaster |
| Characteristics |
tissue: Head
age: day 10 of adulthood
genotype: Elav-Gal4/+;UAS-tauR406W/+
|
| Growth protocol |
Heads of 10 day old control and tauR406W transgenic Drosophila were collected and frozen at -80C prior to RNA extraction.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Trizol extraction followed by RNeasy MinElute Column (Cat No./ID: 74204, Qiagen) clean up.
Extracted RNA was used for stranded library preparation using the Ovation RNA-Seq System for Drosophila (#0350, NuGen) according to the User Guide, including depletion of Drosophila rRNAs. RNA libraries were prepared for sequencing using standard Illumina protocols.
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 3000 |
| |
|
| Description |
rRNA depleted
|
| Data processing |
RNA-sequencing was performed by the Genome Sequencing Facility at Greehey Children’s Cancer Research Institute at the University of Texas Health San Antonio
Raw FASTQ files underwent quality control and were trimmed with Trimmomatic v.0.36
FastQC was used to evaluate the quality of the reads before and after trimming
Trimmed FASTQ files were mapped and aligned to the Drosophila melanogaster transcriptome (FlyBase (Thurmond et al., 2019) FB2018_6.27) using Salmon v.0.13.1
Differential expression analysis was performed using DESeq2 v1.24
Genome_build: dm6
Supplementary_files_format_and_content: Matrix table with normalized gene counts for every gene and every sample
|
| |
|
| Submission date |
Jun 11, 2020 |
| Last update date |
Jun 29, 2020 |
| Contact name |
Paulino Ramirez |
| Organization name |
University of Texas Health San Antonio
|
| Street address |
7703 Floyd Curl Dr
|
| City |
San Antonio |
| ZIP/Postal code |
78229 |
| Country |
USA |
| |
|
| Platform ID |
GPL23323 |
| Series (1) |
| GSE152278 |
RNA sequencing of control versus tauR406W transgenic Drosophila heads at day 10 of adulthood |
|
| Relations |
| BioSample |
SAMN15214359 |
| SRA |
SRX8530613 |
