|
| Status |
Public on May 17, 2016 |
| Title |
PEER |
| Sample type |
RNA |
| |
|
| Source name |
PEER
|
| Organism |
Homo sapiens |
| Characteristics |
cell line: PEER
cell type: other
|
| Growth protocol |
Cells were grown in RPMI supplemented with 10% or 20% (ALL-SIL) fetal bovine serum, 1% glutamin and 1% penicilin/streptomycin
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA was harvested with the miRNeasy mini kit (Qiagen) with Dnase treatment on-column.
|
| Label |
Cy3
|
| Label protocol |
Cyanine-3 (Cy3) labeled cRNA was prepared from 100 ng RNA using the One-Color Low Input Quick Amp Labling kit (Agilent) according to the manufacturer's instructions, followed by miRNeasy column purification (Qiagen). Dye incorporation and cRNA yield were checked with the NanoDrop ND-1000 Spectrophotometer.
|
| |
|
| Hybridization protocol |
600 ng of Cy3-labelled cRNA (specific activity >6 pmol Cy3/ug cRNA) was fragmented at 60°C for 30 minutes in a reaction volume of 25µl containing 1x Agilent fragmentation buffer and 2x Agilent blocking agent following the manufacturers instructions. On completion of the fragmentation reaction, 25 µl of 2x GEx Hybridization buffer HI-RPM was added to the fragmentation mixture and hybridized to the array for 17 hours at 65°C in a rotating hybridization oven. After hybridization, microarrays were washed 1 minute at room temperature with GE Wash Buffer 1 (Agilent) and 1 minute with 37°C GE Wash buffer 2 (Agilent).
|
| Scan protocol |
Slides were scanned immediately after washing on the Agilent DNA Microarray Scanner with SureScan High-Resolution Technology using one color scan setting for 8x60k array slides (Scan Area 61x21.6 mm, Scan resolution 3µm, Dye channel is set to Green).
|
| Description |
Gene expression of PEER cell line
|
| Data processing |
The scanned images were analyzed with Feature Extraction Software 9.1 (Agilent) using default parameters (protocol GE1-105_Dec08 and Grid: 041648_D_F_20120615) to obtain background subtracted and spatially detrended Processed Signal intensities. Normalization was performed using the VSN-package (Bioconductor) and background correction was performed during the normalization process, selecting those probes detecting a 10% higher expression than the negative control probes of the array design in at least one treatment.
|
| |
|
| Submission date |
Oct 22, 2015 |
| Last update date |
May 17, 2016 |
| Contact name |
Annelynn Wallaert |
| E-mail(s) |
annelynn.wallaert@ugent.be
|
| Organization name |
UGent
|
| Street address |
De Pintelaan 185
|
| City |
Gent |
| ZIP/Postal code |
9000 |
| Country |
Belgium |
| |
|
| Platform ID |
GPL19197 |
| Series (2) |
| GSE74272 |
The role of long noncoding RNAs in T-cell acute lymphoblastic leukemia |
| GSE74312 |
Long noncoding RNA signatures define oncogenic subtypes in T-cell acute lymphoblastic leukemia |
|
