|
| Status |
Public on Sep 16, 2018 |
| Title |
A673_siRNA6_2 |
| Sample type |
SRA |
| |
|
| Source name |
Ewing sarcoma cells
|
| Organism |
Homo sapiens |
| Characteristics |
cell line: A673
cell type: Ewing sarcoma
|
| Treatment protocol |
The siRNA molecules (final concentration 13 nM) were reverse transfected to the cells using siLentFect transfection reagent.
|
| Growth protocol |
Cells were grown in DMEM (high Glucose 4.5g/l) supplemented with 10% Tet system Approved Fetal Bovine Serum, L-glutamine, penicillin and streptomycin, 50 µg/ml Zeocin and 2 µg/ml blasticidine S hydrochloride.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
RNA was isolated 48 hours after transfection from three independent experiments using RNeasy RNA isolation kit (Qiagen) with DNase treatment (Qiagen)
Library preparation was done according to Illumina TruSeq® RNA Sample Preparation v2 Guide
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 2500 |
| |
|
| Description |
siLRWD1-6, series 2
|
| Data processing |
The base calling was done using bcl2fastq (v1.8.4)
Read alignment was done using TopHat (v2.0.10) to hg19 human genome reference
Genewise read counts were calculated using HTSeq (v0.5.4p3)
Genome_build: hg19
Supplementary_files_format_and_content: countdata.txt is a tab delimited text file and contains the genewise read counts across samples.
|
| |
|
| Submission date |
Sep 16, 2015 |
| Last update date |
May 15, 2019 |
| Contact name |
Kristiina Iljin |
| E-mail(s) |
kristiina.iljin@vtt.fi
|
| Organization name |
VTT
|
| Street address |
Tietotie 2
|
| City |
Espoo |
| ZIP/Postal code |
02044 |
| Country |
Finland |
| |
|
| Platform ID |
GPL16791 |
| Series (1) |
| GSE73092 |
High-throughput RNAi cell viability screen to identify selective targets for EWS-FLI1 positive Ewing sarcoma |
|
| Relations |
| BioSample |
SAMN04090309 |
| SRA |
SRX1250328 |
