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Sample GSM989229 Query DataSets for GSM989229
Status Public on Aug 22, 2012
Title spermatocytes_control_biological rep1
Sample type RNA
 
Source name untreated, isolated mouse spermatogenic cells enriched with spermatocytes (~80%)
Organism Mus musculus
Characteristics strain: FVB/N
gender: male
age: 10-16-week-old
tissue type: testes
cell type: spermatocytes
Treatment protocol untreated (control)
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 untreated cells sensitive to damage in elevated temperatures (spermatocytes)
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

Data table header descriptions
ID_REF
VALUE log2 RMA signal.

Data table
ID_REF VALUE
11287_at 5.29
11298_at 7.00
11302_at 5.57
11303_at 4.95
11304_at 5.64
11305_at 6.50
11306_at 3.85
11307_at 5.61
11308_at 4.63
11350_at 6.59
11352_at 6.15
11354_at 5.54
11363_at 5.46
11364_at 5.63
11370_at 8.21
11409_at 6.76
11416_at 6.46
11418_at 6.30
11419_at 7.23
11421_at 9.11

Total number of rows: 17306

Table truncated, full table size 244 Kbytes.




Supplementary file Size Download File type/resource
GSM989229_SC_C_1.CEL.gz 3.9 Mb (ftp)(http) CEL
Raw data provided as supplementary file
Processed data included within Sample table

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