|
| Status |
Public on Jun 25, 2009 |
| Title |
EBV transformed lymphoblastoid cell line (mRNA, Sample 2) |
| Sample type |
RNA |
| |
|
| Source name |
EBV transformed lymphoblastoid cell line
|
| Organism |
Homo sapiens |
| Characteristics |
cell line: EBV transformed lymphoblastoid cell line
pathological grade: low grade
|
| Treatment protocol |
Natural grown cell lines without any treatment
|
| Growth protocol |
We then grew all transformed cell lines in RPMI 1640 media supplemented with 15% fetal bovine serum, and 1% penicillin/streptomycin at 37°C in humidified incubators in an atmosphere of 5% CO2. Experimental series were set up by seeding 5-ml cultures in T25 flasks. Each culture was fed with 5ml of fresh media twice a week until the cell number reached ~106 in a T75 flask. The cells were harvested and suspended in 500 l of RNAlater and stored at -80°C for further processing.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
We extracted total RNA from each cell culture using miRNeasy Mini Kit (QIAGEN) under the manufacturer’s guidelines. This protocol could effectively recover both mRNA and miRNA. The integrity of these total RNAs was assessed using an Agilent 2100 Bioanalyzer.
|
| Label |
biotin
|
| Label protocol |
500ng of total RNA was labled using Illumina human-6 V2 BeadChip standard protocol
|
| |
|
| Hybridization protocol |
Illumina human-6 V2 BeadChip standard protocol
|
| Scan protocol |
Illumina BeadArray reader
|
| Description |
cell line from a patient with prostate cancer
|
| Data processing |
We first transformed raw data generated from BeadStudio (Illumina, San Diego, CA) using a variance stabilization transformation algorithm and then normalized them using quantile normalization implemented in Bioconductor (www.bioconductor.org).
|
| |
|
| Submission date |
Feb 11, 2009 |
| Last update date |
Feb 03, 2010 |
| Contact name |
LIANG WANG |
| E-mail(s) |
wang.liang@mayo.edu
|
| Organization name |
MAYO CLINIC
|
| Department |
LAB MED PATH
|
| Street address |
200 FIRST ST SW
|
| City |
Rochester |
| State/province |
MN |
| ZIP/Postal code |
55905 |
| Country |
USA |
| |
|
| Platform ID |
GPL6102 |
| Series (2) |
| GSE14794 |
Genome-wide Transcriptional Profiling Reveals MicroRNA-correlated Genes and Pathways in Human Lymphoblastoid Cell Lines |
| GSE20161 |
Networks and miRNAs implicated in aggressive prostate cancer |
|
