|
| Status |
Public on Dec 31, 2017 |
| Title |
c3 |
| Sample type |
SRA |
| |
|
| Source name |
melanoma cell line
|
| Organism |
Homo sapiens |
| Characteristics |
cell line: 1205Lu
tumor stage: metastatic
treatment: pCMV6
|
| Treatment protocol |
7.8 µg plasmid DNA (pCMV6-SOX10 or pCMV6 control) per flask were transiently transfected using 23.5 µl FuGENE® 6 transfection reagent (Promega, Madison, Wisconsin, USA) in 366 µl Opti-MEM reduced serum medium (Gibco by life technologies, Carlsbad, California, USA) and 7.8 ml Tu2% medium on top of the cells. Twenty-four hours later, cells were harvested in 1 ml QIAzol (Qiagen, Hilden, Germany).
|
| Growth protocol |
1x106 1205Lu metastatic melanoma cells were seeded in a T75 flask and cultivated overnight at 37°C and 5% CO2 in Tu2% medium.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA was isolated with DirectZol Kit (Zymo Research) according to the accompanying instructions
125 ng of total RNA were used for library construction with Nugen Encore Complete RNAseq library system following the manufacturer's protocol
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 1500 |
| |
|
| Data processing |
Basecalling was done by RTA1.17.21.3
reads were mapped to the plasmid used for transfection in order to remove reads derived from residual plasmid DNA. Unmapped reads were used as input for the further steps
reads were aligned to the human genome by Tophat v1.4.0 with hg19 and a gtf file with gene annotations downloaded from the igenomes website (http://support.illumina.com/sequencing/sequencing_software/igenome.html)
reads overlapping with annotated genes were counted with HTseq count
variance stabilisation and differential gene expression were done by DESeq
Genome_build: hg19
Supplementary_files_format_and_content: raw count table from HTseq count
|
| |
|
| Submission date |
Apr 06, 2016 |
| Last update date |
May 15, 2019 |
| Contact name |
Stefan Krebs |
| E-mail(s) |
krebs-st@lmb.uni-muenchen.de
|
| Phone |
0049-89-2180 76715
|
| Organization name |
Ludwig-Maximilian University
|
| Department |
Gene Center
|
| Lab |
Lafuga Genomics
|
| Street address |
Feodor-Lynen-Str. 25
|
| City |
Munich |
| ZIP/Postal code |
81377 |
| Country |
Germany |
| |
|
| Platform ID |
GPL18460 |
| Series (1) |
| GSE79988 |
The myelin protein PMP2 is regulated by SOX10 and drives melanoma cell invasion |
|
| Relations |
| BioSample |
SAMN04621351 |
| SRA |
SRX1684208 |
