|
| Status |
Public on Jun 30, 2024 |
| Title |
S2 cells control input 3 |
| Sample type |
SRA |
| |
|
| Source name |
S2 cells
|
| Organism |
Drosophila melanogaster |
| Characteristics |
cell line: S2 cells
cell type: Embryonic hemocytes
genotype: WT
treatment: Effectene alone
fraction: total cell lysate
|
| Treatment protocol |
Transfection using effectene reagent with 7.5 μg of dsRNA for RpS19a for 72 hours before collection for polysome profiling.
|
| Growth protocol |
S2 cells grown in in Gibco Schneider’s S2 cell medium with 10% FBS, at 28°C
|
| Extracted molecule |
polyA RNA |
| Extraction protocol |
Extraction using a Promega Reliaprep mini extraction kit. RNA was eluted in 30 μl nuclease-free water, RNA quality was checked using an Agilent Bioanalyzer and RNA concentration was measured using Qubit RNA (broad range) reagents. 1 μg of RNA in 50 μl nuclease-free water was used to prepare sequencing libraries
RNA was prepared using the standard TruSeq Illumina protocol, with Oligo-dT beads used to enrich for mRNA
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina NextSeq 500 |
| |
|
| Data processing |
Sequence quality was verified using FastQC
The first 10 bases were trimmed using Trimmomatic using sliding-window approach
Alignment was performed using HiSAT2
Gene-level counts were performed using featureCounts
Analysis of differential translation was performed using anota2seq package with normalize = TRUE and filterZeroGenes = TRUE options enabled. The anota2seq “batchVec” option was used to correct for batch effects between technical triplicates
Assembly: Drosophila melanogaster Ensembl genome BDGP6
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 anota2seq (differential translation). Each column contains: ID, apvSlope, apvSlopeP, apvEff, apvRvmMSerror, apvRvmF, residRvmDf, apvRvmP, apvRvmPAdj, singleRegMode
|
| |
|
| 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 |
GPL19132 |
| Series (2) |
| GSE236307 |
RpS19a depletion alters the haematopoietic translatome to directly drive tissue overgrowth I |
| GSE236312 |
RpS19a depletion alters the haematopoietic translatome to directly drive tissue overgrowth |
|
| Relations |
| BioSample |
SAMN36183122 |
| SRA |
SRX20853817 |
