|
| Status |
Public on Aug 22, 2012 |
| Title |
spermatocytes_heat shock_38_biological rep3 |
| Sample type |
RNA |
| |
|
| Source name |
isolated mouse spermatogenic cells enriched with spermatocytes (~80%), heat shock: 38°C
|
| Organism |
Mus musculus |
| Characteristics |
strain: FVB/N
gender: male
age: 10-16-week-old
tissue type: testes
cell type: spermatocytes
|
| Treatment protocol |
heat shock performed on isolated cells at 38°C for 1 hour and 2 hours of recovery at physiological temperature (32°C)
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Spermatocytes were isolated by unit gravity sedimentation of spermatogenic cells (obtained after collagenase type IA/trypsin/DNase I digestion of decapsulated testes) in 1-3% w/v linear BSA gradient. Finally cells were suspended in RPMI medium supplemented with 10% fetal bovine serum, , 0.004% gentamycin and 6mM sodium lactate
Total RNA was isolated using RNeasy® Mini Kit spin columns (Qiagen) according to the manufacturer's instructions.
|
| Label |
biotin
|
| Label protocol |
cDNA was synthesized from 8 ug of total RNA using the One-Cycle cDNA Synthesis Kit with SuperScriptII polymerase then reverse-transcribed with a T7 RNA polymerase incorporating biotin-labeled nucleotides using the GeneChip IVT Labeling Kit.
|
| |
|
| Hybridization protocol |
Biotin-labeled cRNA probe samples were purified, fragmented and hybridized (without DMSO) at 45°C overnight to the Affymetrix GeneChip® Mouse Genome 430 2.0 Array. The arrays were washed and stained in the Affymetrix Fluidics Station.
|
| Scan protocol |
The arrays were scanned using a microarray scanner, which is component of the Affymetrix GeneChip Instrument System
|
| Description |
Gene expression data from cells sensitive to damage in elevated temperatures (spermatocytes) after a mild heat shock treatment
|
| Data processing |
The data was analyzed with R/Bioconductor and Matlab softwares, RMA algorithm with Dai annotation (Brainarray, version 15.1 dated Jan 2012) were used for data normalization.
|
| |
|
| Submission date |
Aug 21, 2012 |
| Last update date |
Oct 22, 2012 |
| Contact name |
Joanna Polanska |
| E-mail(s) |
joanna.polanska@polsl.pl
|
| Phone |
+48322372144
|
| Organization name |
Silesian University of Technology
|
| Department |
Automatic Control
|
| Lab |
Data Mining Group
|
| Street address |
Akademicka 16
|
| City |
Gliwice |
| ZIP/Postal code |
44-100 |
| Country |
Poland |
| |
|
| Platform ID |
GPL15967 |
| Series (1) |
| GSE40248 |
Expression data from control and heat shocked mouse spermatocytes and hepatocytes |
|
