|
| Status |
Public on Dec 01, 2018 |
| Title |
PA-1 |
| Sample type |
SRA |
| |
|
| Source name |
Fly heads
|
| Organism |
Drosophila melanogaster |
| Characteristics |
genotype/variation: Elav>PA36
age: 5 days
Sex: Female
tissue: Head
|
| Growth protocol |
All flies were maintained at 24 °C on a 12:12 hour light:dark cycle at 60% humidity on a standard medium.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Four groups of flies (control PA36, (G4C2)36, PR36, UPF1-RNAi) were used for RNA-Seq. Each genotype contains two replicates with total 40 female fly heads. RNA was extracted by Trizol reagent (Thermo Fisher Scientific). Whole transcriptome libraries preparation and sequencing were performed by Annoroad Gene Technology Corporation (Beijing, China).
RNA libraries were prepared for sequencing using standard Illumina protocols.
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
HiSeq X Ten |
| |
|
| Description |
mRNA
processed data file: hisat_TPM_result_2018-07-23.txt
|
| Data processing |
Illumina bcl2fastq software was used for basecalling.
The FASTQ files containing raw sequence reads were aligned to fruit fly genome (BDGP6) by HISAT2 program (Version 2.1.o, default parameters). The number of reads mapped to each transcript were also calculated by HISAT2 (default parameters) based on the gene annotations from Ensembl Release 93 (www.ensembl.org).
The read numbers were Transcripts Per Kilobase Million (TPM) from HISAT2 result file. Compared with control PA36 group, genes with P-value<0.05 and |log2-transformed fold change|>1 were considered as differentially expressed.
Genome_build: BDGP6
Supplementary_files_format_and_content: hisat_TPM_result_2018-07-23.txt: Tab-delimited text file includes TPM values for all samples.
|
| |
|
| Submission date |
Nov 30, 2018 |
| Last update date |
Dec 03, 2018 |
| Contact name |
Wangchao Xu |
| E-mail(s) |
m13918657749@163.com
|
| Phone |
86-21-54921752
|
| Organization name |
Institute of Neuroscience
|
| Street address |
320 Yue Yang Road
|
| City |
shanghai |
| State/province |
shanghai |
| ZIP/Postal code |
200031 |
| Country |
China |
| |
|
| Platform ID |
GPL23702 |
| Series (1) |
| GSE123172 |
Activation of nonsense-mediated mRNA decay protects against C9orf72 dipeptide-repeat neurotoxicity |
|
| Relations |
| BioSample |
SAMN10505115 |
| SRA |
SRX5084424 |
