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Sample GSM722122 Query DataSets for GSM722122
Status Public on May 09, 2014
Title Ttf+/+T43H_15d_rep3
Sample type RNA
 
Source name Ttf+/+T43H, testes, 15 ppt
Organism Mus musculus
Characteristics strain: C57BL/10J-Ttf+/+T43H
gender: male
age: 15 days
tissue: testes
Treatment protocol Mice were euthanized by cervical dislocation. For isolation of spermatogenic populations the single cell suspension from testicular tubules was prepared and the populations were isolated using fluorescence activated cell sorting of testicular single cell suspension according to ref. (Bastos et al. 2005). Testicular RNA from 15 days old animals was isolated from the testes after removal of tunica.
Growth protocol Mouse lines used in the experiment were C57BL/6J , C57BL/10J, C57BL/10J -Ttf+/+T43H and C57BL/10J - t12+/+T43. All the male mice used for isolation of spermatogenic populations were two months old. 15 days old males were used for comparison of testicular expression.
Extracted molecule total RNA
Extraction protocol Total RNA from individual populations was isolated using RNeasy Micro kit (Qiagen) according to manufacturer‘s protocol. Testicular RNA from 15 days old males was isolated using RNeasy Mini isolation kit (Qiagen) according to manufacturer‘s protocol.
Label biotin
Label protocol Between 20 to 30 ng of total RNA were used to prepare biotinylated cRNA according to the standard Affymetrix Two-Cycle protocol (Expression Analysis Technical Manual, 701021 Rev. 5, Affymetrix).
 
Hybridization protocol Following fragmentation, 15 ug of cRNA were hybridized for 16 hr at 45°C on GeneChip Mouse Genome 430 2.0 Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.
Scan protocol GeneChips were scanned using the GeneChip Scanner 3000 7G.
Data processing The data were analyzed independently for spermatogenic populations and testicular samples from 15 days old animals. The analysis was done with Bioconductor and R statistics (version 2.12) using the gcRMA method with default settings and custom chip description file (probes were annotated to Entrez identifiers - NCBI build 37) mm430mmentrezg, created by Microarray Lab at the Molecular and Behavioral Neuroscience Institute at the University of Michigan.
 
Submission date May 10, 2011
Last update date May 09, 2014
Contact name David Homolka
E-mail(s) david.homolka@img.cas.cz
Organization name Institute Of Molecular Genetics
Department Department of Mouse Molecular Genetics
Street address Videnska 1083
City Prague 4
ZIP/Postal code 142 20
Country Czech Republic
 
Platform ID GPL7546
Series (1)
GSE29177 Meiotic Consequences of Genetic Extension of Unsynapsed Autosomal Chromatin

Data table header descriptions
ID_REF
VALUE gcRMA values (log2)

Data table
ID_REF VALUE
100009600_at 4.950065628
100012_at 2.384354542
100017_at 6.630359629
100019_at 9.217930739
100034251_at 5.2290066
100036521_at 10.16617017
100037258_at 9.891425988
100037278_at 5.768178417
100038570_at 9.660224886
100038635_at 2.519347909
100038680_at 1.555975996
100038887_at 14.21135971
100038959_at 2.548225548
100039026_at 7.270406147
100039027_at 2.442124925
100039094_at 1.731948374
100039235_at 1.719887859
100039282_at 2.637971681
100039284_at 3.818813955
100039307_at 1.823012963

Total number of rows: 16539

Table truncated, full table size 343 Kbytes.




Supplementary file Size Download File type/resource
GSM722122.CEL.gz 3.6 Mb (ftp)(http) CEL
Processed data included within Sample table

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