|
| Status |
Public on Jul 17, 2024 |
| Title |
DfJ5KO mbt male C |
| Sample type |
SRA |
| |
|
| Source name |
larval brain
|
| Organism |
Drosophila melanogaster |
| Characteristics |
tissue: larval brain
genotype: DfJ5_ts1
treatment: male
|
| Extracted molecule |
polyA RNA |
| Extraction protocol |
RNA was isolated using magnetic beads (RNAClean XP, Beckman Coulter, A63987) from 10 Drosophila larval brains per sample.
Library preparation were done with NEBNext Ultra RNA II Library Prep Kit for Illumina and NEBNext Multiplex Oligos for Illumina Set 1, 2, and 3 followingthe manufacturer's instructions.
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 2500 |
| |
|
| Data processing |
Data were processed with the Grape RNA-seq pipeline. Raw reads were aligned to the fly genome and transcriptome uding STAR. Genes and transcripts were quantified using RNA-seq by Expectation Maximization (RSEM).
The library size for each sample was scaled according to the TMM (trimmed mean of M values) normalization method.
Expression coverage files in BAM format were generated using STAR (v2.4.0j) and later normalized according to the scaling factors obtained by the TMM normalization method
Assembly: dm6
Supplementary files format and content: tab-delimited text file includes RPKM values for each sample
|
| |
|
| Submission date |
Apr 03, 2024 |
| Last update date |
Sep 20, 2024 |
| Contact name |
Cayetano Gonzalez |
| E-mail(s) |
gonzalez@irbbarcelona.org
|
| Organization name |
IRB Barcelona
|
| Street address |
baldiri Reixac 10
|
| City |
Barcelona |
| ZIP/Postal code |
08028 |
| Country |
Spain |
| |
|
| Platform ID |
GPL17275 |
| Series (1) |
| GSE263157 |
The Drosophila cancer-germline, head-to-head gene pair TrxT and dhd is dispensable for normal brain development but plays a major role in l(3)malignant brain tumour growth. |
|
| Relations |
| BioSample |
SAMN40744659 |
| SRA |
SRX24151390 |
