|
| Status |
Public on May 30, 2021 |
| Title |
Single cell seq S2 cells plate1 |
| Sample type |
SRA |
| |
|
| Source name |
S2 cell
|
| Organism |
Drosophila melanogaster |
| Characteristics |
tissue: S2 cells
treatment: Well 1-6 contains cells treated: 4h induced + 4h Schneider's, well 7-12 contains cells treated: 4h induced + 4h Krebs Ringer Bicarbonate buffer, well 13-18 contains cells treated: 4h induced + 4h 0.5mM sodium arsenite in Schneider's, well 19-23 contains cells treated 2h induced + 2h Schneider's, well 24 is empty
|
| Treatment protocol |
S2 cells were treated with CuSO4 to induce protein expression, neuron expression was induced by RU486. Cells were stressed with 0.5mM sodium arsenite
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Direct-zol RNA microprep kit (Zymo)
See Muraro et al. 2016
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina NextSeq 500 |
| |
|
| Data processing |
tRNA genes and pseudogenes were identified using tRNAscan-SE (version 2.0.7)
Adapter and homopolymer sequences were first trimmed from read 2 using cutadapt (version 3.2)
Trimmed reads were depleted of rRNA sequences by aligning to a ribosomal reference using bwa aln (version 0.7.17-r1188) and bwa mem, and discarding any read that aligned using either method
Depleted reads were then two-pass aligned to the reference genome using STARSolo (version 2.7.7a)
Aligned reads were deduplicated with UMI-tools (version 1.1.1)
Variant identification followed the GATK RNA-seq short variant discovery best-practices workflow using GATK (version 4.1.9.0)
Allele frequency and statistics were determined using an in-house written script
Genome_build: BDGP6
|
| |
|
| Submission date |
May 29, 2021 |
| Last update date |
May 30, 2021 |
| Contact name |
Wessel van Leeuwen |
| E-mail(s) |
[email protected]
|
| Organization name |
Hubrecht Institute
|
| Street address |
Uppsalalaan 8
|
| City |
Utrecht |
| ZIP/Postal code |
3584CT |
| Country |
Netherlands |
| |
|
| Platform ID |
GPL19132 |
| Series (1) |
| GSE175782 |
Identification of the stress granule transcriptome via RNA-editing in bulk S2 cells, single S2 cells and in Drosophila neurons |
|
| Relations |
| BioSample |
SAMN19430157 |
| SRA |
SRX11023258 |
