|
| Status |
Public on Apr 07, 2011 |
| Title |
LAU-Me275 melanoma cells patient LAU50 (454) |
| Sample type |
SRA |
| |
|
| Source name |
Low-passage culture of lymph node metastasis from cutaneous melanoma
|
| Organism |
Homo sapiens |
| Characteristics |
gender: male
cell line: cell derived from metastatic melanoma
source tissue: lymph node
|
| Treatment protocol |
none
|
| Growth protocol |
Melanoma cell lines were cultured in RPMI-1640 medium supplemented with 10% FCS. Normal human melanocytes were grown in HAM-F10 medium supplemented with 2% FCS, 5% MelanoMax supplement (Gentaur, Belgium) and 6 mM HEPES.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
mRNA isolation and cDNA preparation were performed following the protocol used by Bainbridge et al (BMC Genomics. 2006 ). Then 3-5 µg of cDNA were used for 454 libraries preparation, according to manufactures’ procedures.
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
454 GS FLX |
| |
|
| Description |
cDNA was sequenced using single end read with the Roche 454 technology
hg18 used for NHM_7Mel_mRNA_cnt.txt
|
| Data processing |
All experiments produced about 1M single end reads, with a median length of 367 nucleotides (interquartile range 265-436). We derived transcript tag count using the Tromer pipeline described in Jongeneel et al. (PNAS 2003)
|
| |
|
| Submission date |
Jul 14, 2010 |
| Last update date |
May 15, 2019 |
| Contact name |
Armand Valsesia |
| Organization name |
Ludwig Institute for Cancer Research
|
| Street address |
Bâtiment Génopode
|
| City |
Lausanne |
| ZIP/Postal code |
1015 |
| Country |
Switzerland |
| |
|
| Platform ID |
GPL9186 |
| Series (2) |
| GSE22932 |
Genome-Wide Analysis of Somatic Copy Number Alterations and Gene Expression in Metastatic Melanoma: RNA-Seq |
| GSE23056 |
Genome-Wide Analysis of Somatic Copy Number Alterations and Gene Expression in Metastatic Melanoma |
|
| Relations |
| SRA |
SRX025092 |
| BioSample |
SAMN00025389 |
