|
| Status |
Public on Aug 31, 2017 |
| Title |
S2_rep3 |
| Sample type |
SRA |
| |
|
| Source name |
S2 Cell line
|
| Organism |
Drosophila melanogaster |
| Characteristics |
cell line: late embryo-derived cell line
strain: S2-DRSC
genotype: wild type
treatment: 10 microMolar Cu2SO4
|
| Treatment protocol |
Cells were treated with 10 microMolar Copper Sulphate for 24 h prior to chromatin and RNA preparation
|
| Growth protocol |
Cells were grown in T-flasks to a density of not more than 7x10^6 cells/ml in Schneider Medium supplemented with 10% FBS
|
| Extracted molecule |
polyA RNA |
| Extraction protocol |
Chromatin was prepared according to the modENCODE procedure; RNA was extracted with Qiagen Rneasy kit
DNA libraries were prepared according to Illumina's instructions; RNA libraries were prepared for sequencing using standard Illumina protocols
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 2000 |
| |
|
| Description |
RNA-Seq of S2 cells Rep3
|
| Data processing |
Basecalls performed using RTA (Illumina)
RNA-seq reads were aligned to the dm3 genome assembly using CASAVA 9v1.8.2) using module "eland_rna"and counts determined using theCASAVA "variant detection and counting" module
RNA-Seq differentially expressed genes were called using edgeR using a false discovery rate (FDR) cut-off of 10%
Genome_build: dm3
Supplementary_files_format_and_content: Tab-delimited (tsv) text files show raw counts of genes for each sample; XLS file shows the edgeR output of differentially expressed genes upon AbdA expression.
|
| |
|
| Submission date |
Jul 18, 2017 |
| Last update date |
May 15, 2019 |
| Contact name |
Andrew J Saurin |
| E-mail(s) |
[email protected]
|
| Organization name |
IBDM / CNRS
|
| Street address |
Campus de Luminy
|
| City |
Marseille |
| ZIP/Postal code |
13009 |
| Country |
France |
| |
|
| Platform ID |
GPL13304 |
| Series (2) |
| GSE101555 |
Gene expression profiling of S2 cells and S2 cells expressing AbdA |
| GSE101557 |
Expression of Hox transcription factors in Drosophila S2 cells |
|
| Relations |
| Reanalyzed by |
GSM3283815 |
| BioSample |
SAMN07361003 |
| SRA |
SRX3011262 |
