|
| Status |
Public on Nov 27, 2009 |
| Title |
NLPHL_lymph_node_case1 |
| Sample type |
RNA |
| |
|
| Source name |
lymph node affected by NLPHL
|
| Organism |
Homo sapiens |
| Characteristics |
Gender: male, Age: 49, Tissue: lymph node taken at diagnosis affected by nodular lymphocyte predominant Hodgkin's lymphoma, An Arbor Stage: IA, follow-up: 10 years; status at last follow-up: died of squamous cell carcinoma of the larynx
|
| Biomaterial provider |
Department of pathology, University Hospitals Leuven
|
| Treatment protocol |
tissue blocs were kept at -80° till use
|
| Growth protocol |
Fresh frozen tissue blocs were kept at -80° till use. They were transported on dry ice to the cryostat where a number (depending on the size of the bloc) of 20 micron thick sections were cut and put into a labeled, 2.0 ml microcentrifuge tube. At the end an extra 3 micron thick section was taken for HE staining.
|
| Extracted molecule |
cytoplasmic RNA |
| Extraction protocol |
Total RNA was extracted from 20 micron sections of each frozen tissue sample, using the TriZol reagent (Invitrogen, Merelbeke, Belgium) followed by purification using the RNaesy mini kit (Qiagen, Venlo, The Netherlands), according to the manufacturers recommendations. RNA quality, integrity and concentration were measured using a nanodrop spectrophotometer (Nanodrop Technologies, Wilmington, DE, USA).
|
| Label |
biotin
|
| Label protocol |
Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 5 microg total RNA.
|
| |
|
| Hybridization protocol |
Following fragmentation, 10 microg of cRNA were hybridized for 16 hr at 45C and at 60 rounds/min. The GeneChips were washed and stained in the Affymetrix Fluidics Station 400 and 450.
|
| Scan protocol |
GeneChips were scanned using the GeneChip Scanner 3000 7G.
|
| Description |
Nodular lymphocyte predominant Hodgkin's lymphoma affecting a lymph node
|
| Data processing |
Data were normalized using GC-RMA. The package gcrma in Bioconductor was used for this (R version 2.3.1)
|
| |
|
| Submission date |
May 14, 2007 |
| Last update date |
Aug 28, 2018 |
| Contact name |
Rekin's Janky |
| E-mail(s) |
Nucleomics.Bioinformatics@vib.be
|
| Organization name |
VIB
|
| Department |
Nucleomics Core
|
| Street address |
Herestraat 49 Box 816
|
| City |
Leuven |
| ZIP/Postal code |
B-3000 |
| Country |
Belgium |
| |
|
| Platform ID |
GPL570 |
| Series (1) |
| GSE7788 |
Nodular lymphocyte predominant Hodgkin's lymphoma vs T cell/histiocyte rich B cell lymphoma |
|
| Relations |
| Reanalyzed by |
GSE119087 |
