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Sample GSM241204 Query DataSets for GSM241204
Status Public on Nov 07, 2007
Title Thy1+ 2dpp gonocytes control-1
Sample type RNA
 
Source name Thy1+ 2dpp gonocytes 8hr control-1
Organism Mus musculus
Characteristics 129/c57BL/6 male, thy1+ gonocytes isolated from 2 dpp testes and treated with vehicle (ethanol) for 8hr
Extracted molecule total RNA
Extraction protocol Trizol reagent solution
Label biotin
Label protocol Approximately 75 ng total RNA from each sample was used to generate cDNA using the Ovation™ RNA Amplification System V2 (NuGEN, San Carlos, CA) according to the manufacturer’s instructions. Briefly, first and second strand cDNA were synthesized, followed by SPIA™ isothermal linear amplification to generate single stranded antisense cDNA. Single stranded antisense cDNA (3.75 ug) was then enzymatically fragmented and end-labeled with biotin using the FL-Ovation™ cDNA Biotin Module V2 (NuGEN, San Carlos, CA) following the manufactures protocol.
 
Hybridization protocol To detect changes in expression levels for gene transcripts, we used the Mouse Genome 430v2.0 GeneChip™ array (Affymetrix, Santa Clara, CA). This array contains more than 45,000 probe sets representing 39,000 transcripts and variants, and is currently the most comprehensive GeneChip array available for the mouse. Approximately 3.75 ìg of biotin-labeled, fragmented cDNA was hybridized to each array for 18 h at 45 °C. Washes and post hybridization processing were performed using the Fluidics Station 450 (Affymetrix) according to the manufacturers’ instructions, and the GeneChip™ arrays were scanned using a laser confocal slide scanner (GeneChip Scanner 3000, Affymetrix). Array quality was assessed and images were quantified using GeneChip™ Operating Software (GCOS) v1.2 (Affymetrix).
Scan protocol To detect changes in expression levels for gene transcripts, we used the Mouse Genome 430v2.0 GeneChip™ array (Affymetrix, Santa Clara, CA). This array contains more than 45,000 probe sets representing 39,000 transcripts and variants, and is currently the most comprehensive GeneChip array available for the mouse. Approximately 3.75 ìg of biotin-labeled, fragmented cDNA was hybridized to each array for 18 h at 45 °C. Washes and post hybridization processing were performed using the Fluidics Station 450 (Affymetrix) according to the manufacturers’ instructions, and the GeneChip™ arrays were scanned using a laser confocal slide scanner (GeneChip Scanner 3000, Affymetrix). Array quality was assessed and images were quantified using GeneChip™ Operating Software (GCOS) v1.2 (Affymetrix).
Description To detect changes in expression levels for gene transcripts, we used the Mouse Genome 430v2.0 GeneChip™ array (Affymetrix, Santa Clara, CA). This array contains more than 45,000 probe sets representing 39,000 transcripts and variants, and is currently the most comprehensive GeneChip array available for the mouse. Approximately 3.75 ìg of biotin-labeled, fragmented cDNA was hybridized to each array for 18 h at 45 °C. Washes and post hybridization processing were performed using the Fluidics Station 450 (Affymetrix) according to the manufacturers’ instructions, and the GeneChip™ arrays were scanned using a laser confocal slide scanner (GeneChip Scanner 3000, Affymetrix). Array quality was assessed and images were quantified using GeneChip™ Operating Software (GCOS) v1.2 (Affymetrix).
Data processing For each microarray, probe set signal values were initially normalized by scaling to a target intensity of 125.
 
Submission date Nov 05, 2007
Last update date Aug 28, 2018
Contact name Lizhong Yang
E-mail(s) lzyang@wsu.edu
Phone 1-509-335-2240
Fax 1-509-335-9688
URL http://www.wsu.edu/~griswold
Organization name Washington State University
Department School of Molecular Biosciences
Lab Griswold Lab/Center for Reproductive Biology
Street address 531 Fulmer Hall/POB 644660
City Pullman
State/province WA
ZIP/Postal code 99164-4660
Country USA
 
Platform ID GPL1261
Series (1)
GSE9521 Thy1+ 2dpp gonocytes RA regulation
Relations
Reanalyzed by GSE119085

Data table header descriptions
ID_REF
VALUE A measure of the abundance of a transcript
ABS_CALL The call in an absolute analysis that indicates if the transcript was present (P), absent (A), marginal (M) or no call(NC)
DETECTION P-VALUE P-value that indicates the significance level of the detection call

Data table
ID_REF VALUE ABS_CALL DETECTION P-VALUE
AFFX-BioB-5_at 173.535 P 4.42873e-05
AFFX-BioB-M_at 326.819 P 4.42873e-05
AFFX-BioB-3_at 261.175 P 4.42873e-05
AFFX-BioC-5_at 588.756 P 4.42873e-05
AFFX-BioC-3_at 438.29 P 4.42873e-05
AFFX-BioDn-5_at 1330.81 P 4.42873e-05
AFFX-BioDn-3_at 1673.71 P 4.42873e-05
AFFX-CreX-5_at 3789.75 P 5.16732e-05
AFFX-CreX-3_at 3848.19 P 4.42873e-05
AFFX-DapX-5_at 1.29324 A 0.327051
AFFX-DapX-M_at 0.338563 A 0.686307
AFFX-DapX-3_at 0.705504 A 0.485109
AFFX-LysX-5_at 1.61353 A 0.185131
AFFX-LysX-M_at 0.846564 A 0.588627
AFFX-LysX-3_at 0.218299 A 0.783476
AFFX-PheX-5_at 0.421646 A 0.617401
AFFX-PheX-M_at 0.321162 A 0.772364
AFFX-PheX-3_at 0.549351 A 0.672921
AFFX-ThrX-5_at 0.213098 A 0.86866
AFFX-ThrX-M_at 0.405927 A 0.686277

Total number of rows: 45101

Table truncated, full table size 1423 Kbytes.




Supplementary file Size Download File type/resource
GSM241204.CEL.gz 3.9 Mb (ftp)(http) CEL
GSM241204.CHP.gz 237.3 Kb (ftp)(http) CHP
Processed data provided as supplementary file
Processed data included within Sample table

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