|
| Status |
Public on Jun 30, 2024 |
| Title |
Lymph glands RpS19a RNAi 1 |
| Sample type |
SRA |
| |
|
| Source name |
Lymph gland
|
| Organism |
Drosophila melanogaster |
| Characteristics |
tissue: Lymph gland
developmental stage: Larval third instar
cell type: hemocyte
genotype: Hemese-GAL4/RpS19a RNAi (VDRC #107188)
treatment: culture at 25°C
|
| Treatment protocol |
UAS-RNAi expression prior to microdissection of larval lymph glands (approximately 120 control lymph glands, or 40 RpS19a RNAi lymph glands were pooled for each sample)
|
| Growth protocol |
Hemese-GAL4 virgin females were crossed to either w1118 or RpS19a RNAi males and the offspring were maintained at 25°C prior to sample collection at larval 3rd instar stage
|
| Extracted molecule |
polyA RNA |
| Extraction protocol |
Promega ReliaPrep RNA Tissue miniprep system (Z6010) following the manufacturer’s protocol and eluted in 15 μL nuclease-free water. RNA purity and integrity were assessed using an automated electrophoresis system (2200 TapeStation, Agilent Technologies)
RNA was prepared using the standard TruSeq Illumina protocol preserving strandedness information, with Oligo-dT beads used to enrich for mRNA
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 2500 |
| |
|
| Data processing |
Sequence quality was verified using FastQC v0.11.6
Alignment was performed using Tophat2 2.0.13
Gene counts were performed using HTSeq 0.6.1
Significant differential expression was analysed using DESeq2 1.12.0
Assembly: dmel-r6.10 (Flybase)
Supplementary files format and content: Plain text (.txt) files containing raw gene-level counts for each sample
Supplementary files format and content: Microsoft Excel (.xlsx) file containing output of DESeq2 (differential gene expression). Each column contains: FlybaseID, baseMean, log2FoldChange, lfcSE, stat, pvalue, padj, geneSymbol, EntrezID
|
| |
|
| Submission date |
Jun 30, 2023 |
| Last update date |
Jun 30, 2024 |
| Contact name |
Olga Zaytseva |
| E-mail(s) |
[email protected]
|
| Organization name |
John Curtin School of Medical Research
|
| Street address |
131 Garran Road
|
| City |
Canberra |
| State/province |
ACT |
| ZIP/Postal code |
2601 |
| Country |
Australia |
| |
|
| Platform ID |
GPL17275 |
| Series (2) |
| GSE236310 |
RpS19a depletion alters the haematopoietic translatome to directly drive tissue overgrowth II |
| GSE236312 |
RpS19a depletion alters the haematopoietic translatome to directly drive tissue overgrowth |
|
| Relations |
| BioSample |
SAMN36183468 |
| SRA |
SRX20853833 |
