|
| Status |
Public on Feb 15, 2017 |
| Title |
TDP43/2U:S14 |
| Sample type |
SRA |
| |
|
| Source name |
TDP43/2U_head
|
| Organism |
Drosophila melanogaster |
| Characteristics |
strain: 2U
tissue: head
genotype/variation: TDP43/2U
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Fly heads were collected for each genotype and total RNA was purified with Trizol (Invitrogen).
RNA-Seq libraries were constructed using the NuGEN Ovation Drosophila RNA-Seq kit including DNase treatmen with HL-dsDNase (ArcticZymes Cat. # 70800-201) and cDNA fragmenation using the Covaris E220 system according to manufacturer recommendations. After amplification library quality was measured using the Agilent Bioanalyzer system and quantity was determined using Life Technologies Qubit dsDNA HS Assay kit (for use with the Qubit 2.0 Fluorometer). Prior to sequencing pooled libraries were quantified using the Illumina Library Quantification kit (with Universal qPCR mix) from Kapa Biosystems and a 1.2 pM loading concentration was used for PE101 on the Illumina NextSeq500 platform.
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina NextSeq 500 |
| |
|
| Data processing |
Reads were mapped to the Drosophila dm3 genome with STAR allowing up to 4 mismatches and a maximum of 100 multiple alignments.
Reads were annotated based on genomic locations against ribosomal RNAs, transposable elements (FlyBase), and RefSeq genes (UCSC genome database RefSeq track).
Reads mapped to ribosomal RNAs were removed from each library. For the remaining reads, expression abundance estimation and differential expression analysis were performed using the TEtranscripts package.
Genome_build: dm3
Supplementary_files_format_and_content: raw counts of sequencing reads for the genes/TEs
|
| |
|
| Submission date |
Aug 09, 2016 |
| Last update date |
May 15, 2019 |
| Contact name |
Wen-Wei Liao |
| Organization name |
Cold Spring Harbor Laboratory
|
| Street address |
1 Bungtown Road
|
| City |
Cold Spring Harbor |
| State/province |
New York |
| ZIP/Postal code |
11724 |
| Country |
USA |
| |
|
| Platform ID |
GPL19132 |
| Series (1) |
| GSE85398 |
Retrotransposon Activation Contributes to Neurodegeneration in a Drosophila TDP-43 Model of ALS |
|
| Relations |
| Reanalyzed by |
GSM3281738 |
| BioSample |
SAMN05553118 |
| SRA |
SRX2010814 |
