|
| Status |
Public on Jan 01, 2018 |
| Title |
Peripheral T-cell lymphoma 17 |
| Sample type |
RNA |
| |
|
| Source name |
Peripheral T-cell lymphoma 17
|
| Organism |
Homo sapiens |
| Characteristics |
tissue: lymph node
disease status: peripheral T cell lymphoma (PTCL)
|
| Growth protocol |
Samples were frozen to preserve the RNA properties.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA was extracted by Trizol reagent (Invitrogen, Carlsbad, CA, USA)
|
| Label |
Cy3
|
| Label protocol |
100ng of total RNA were dephosphorilated, desnaturalizated, treated with ligase T4 and labelled with Cy3 for 2 hours at 16ºC.
|
| |
|
| Hybridization protocol |
Hybridization settings: 20 hours, at 55ºC, at 20rpm. Blocking agent, hybridization and washing buffers was performed according to agilent recomandation.
|
| Scan protocol |
Slides were scanned immediately after washing on the Agilent DNA Microarray Scanner (G2565AA).
|
| Description |
Non-coding RNA profiling by array
SAMPLE 21
|
| Data processing |
The scanned images were analyzed with Feature Extraction Software 9.1 (Agilent) using default parameters (protocol GE1-v1_91 and Grid: 012391_D_20060331) to obtain background subtracted and spatially detrended Processed Signal intensities. Data are normalized to the median of the series (between arrays) by R program version 2.4, (available at http://www.r-project.org/). For normalization was used the "Processed Signal" of the feature extraction files (already includes background subtraction) was used. Average of miRs replicates was then applied using the following web page: http://prep.bioinfo.cnio.es/. Significance Analysis of Microarray excel macro (SAM) was used.
|
| |
|
| Submission date |
Nov 08, 2016 |
| Last update date |
Jan 01, 2018 |
| Contact name |
Rebeca Manso |
| E-mail(s) |
rebeca.manso@fjd.es
|
| Organization name |
Fundación Jiménez Díaz
|
| Department |
Pathology
|
| Street address |
Av. Reyes Católicos, 2
|
| City |
Madrid |
| State/province |
Madrid |
| ZIP/Postal code |
28040 |
| Country |
Spain |
| |
|
| Platform ID |
GPL8227 |
| Series (1) |
| GSE89671 |
BCL6 expression in AITL could be transcriptionally regulated |
|
