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Sample GSM2109663 Query DataSets for GSM2109663
Status Public on Dec 31, 2017
Title s1
Sample type SRA
Source name melanoma cell line
Organism Homo sapiens
Characteristics cell line: 1205Lu
tumor stage: metastatic
treatment: pCMV6-SOX10
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 (
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
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
BioSample SAMN04621346
SRA SRX1684203

Supplementary data files not provided
SRA Run SelectorHelp
Raw data are available in SRA
Processed data are available on Series record

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