|
| Status |
Public on Aug 14, 2019 |
| Title |
WT_4d rep2 |
| Sample type |
SRA |
| |
|
| Source name |
Imaginal wing disc
|
| Organism |
Drosophila melanogaster |
| Characteristics |
strain: FRT82B (BL2035)
tissue: Imaginal wing disc
age: After Egg Laying 4d
genotype: FRT82B
|
| Growth protocol |
Around 50 embryos collected within 3 hours were put in an individual vial of fly food to avoid crowding and the larvae were raised at 25-degree incubator for appropriate lengths of time before dissection.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA was extracted from control and scrib¹ wing imaginal discs with RNeasy Mini Kit (Qiagen).
Construction of cDNA libraries and 150bp paired-end sequencing on Illumina HiSeq platform were performed by Novogene.
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 4000 |
| |
|
| Data processing |
Cleaned raw reads were mapped to the reference genome using STAR with settings: --outFilterMultimapNmax 20 --outFilterMultimapScoreRange 1 --outFilterScoreMinOverLread 0.33 \ --outFilterMatchNminOverLread 0.33 --outFilterMismatchNmax 10 --alignIntronMax 100000 --alignMatesGapMax 1000000 \ --alignSJDBoverhangMin 1 --sjdbOverhang 149 --sjdbScore 2 \ (Dobin et al., 2013).
Counts are generated by featureCounts available in Subread package (Liao et al., 2013).
Count normalization was performed using edgeR (Robinson et al., 2010).
Genome_build: GCF_000001215.4
Supplementary_files_format_and_content: txt files include Computes counts per million (CPM) values for each Sample
|
| |
|
| Submission date |
Apr 24, 2019 |
| Last update date |
Aug 17, 2019 |
| Contact name |
Yan Yan |
| E-mail(s) |
drosophilaust@gmail.com
|
| Organization name |
HKUST
|
| Department |
LIFS
|
| Street address |
Clear Water Bay
|
| City |
Hong Kong |
| ZIP/Postal code |
999077 |
| Country |
China |
| |
|
| Platform ID |
GPL21306 |
| Series (1) |
| GSE130243 |
Quantitative Analysis of Wild Type and scrib mutant Drosophila wing imaginal discs Transcriptomes at different time points |
|
| Relations |
| BioSample |
SAMN11490227 |
| SRA |
SRX5729115 |
