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Sample GSM923297 Query DataSets for GSM923297
Status Public on Jul 22, 2013
Title rat hippocampus (CA1 region), sham, 18 months old, subject 9
Sample type RNA
 
Source name rat hippocampus (CA1 region)_sham
Organism Rattus norvegicus
Characteristics strain: Fisher 344
gender: male
age: 18 months
tissue: hippocampal CA1 brain
treament group: sham
Extracted molecule total RNA
Extraction protocol RNA was extracted from each CA1 tissue block, as described previously (Blalock et al., 2003; Kadish et al., 2009; Rowe et al., 2007) using TRIzol (Invitrogen) followed by ethanol precipitation, and was reconstituted in RNase-free water (Standard Affymetrix)
Label biotin
Label protocol For each sample, 20 ug of biotin-labeled cRNA was generated from 5 ug of total RNA according to manufacturer’s instructions (Standard Affymetrix).
 
Hybridization protocol Standard Affymetrix- 20 ug biotin-labeled cRNA was applied to a rat RGU34A GeneChip (Affymetrix) for hybridization (one chip per animal).
Scan protocol Standard Affymetrix
Description hippocampus CA1 region
Data processing The data were analyzed for quality control with Microarray Suite version 5.0 (MAS 5.0) using Affymetrix default analysis settings. Robust Multi-Chip Analysis (RMA) was used to generate signal intensity values using the standard settings in Bioconductor (2.2) operating in the R programming environment (R 2.7.1) with the 'justRMA' command.
 
Submission date Apr 26, 2012
Last update date Jul 24, 2013
Contact name Eric M Blalock
E-mail(s) eric.blalock@uky.edu
Phone 859-323-8033
Organization name University of Kentucky
Department Molecular and Biomedical Pharmacology
Lab Blalock
Street address 800 Rose St.
City Lexington
State/province KY
ZIP/Postal code 40475
Country USA
 
Platform ID GPL85
Series (1)
GSE37618 Glucocorticoid-Dependent Hippocampal Transcriptome in Male Rats: Pathway-Specific Alterations with Aging

Data table header descriptions
ID_REF
VALUE RMA-calculated Signal intensity

Data table
ID_REF VALUE
rc_AI231778_at 7.2569
rc_AA894262_at 6.68978
AF050659UTR#1_at 6.58894
AF030086UTR#1_at 4.50081
J01878_at 8.807
rc_AA859994_at 7.78243
X62950mRNA_f_at 7.30339
X53231_at 7.22262
M13100cds#1_g_at 7.89132
rc_AA859680_at 7.75668
D83349_at 9.56723
rc_AA891596_at 4.48596
U18419_at 5.22241
M81183Exon_UTR_g_at 3.8716
U48828_g_at 8.94701
rc_AI010292_s_at 12.6573
M23890_s_at 6.98925
rc_AI175776_s_at 4.4038
AF050664UTR#1_at 6.68682
AF057564_at 5.77496

Total number of rows: 8799

Table truncated, full table size 182 Kbytes.




Supplementary file Size Download File type/resource
GSM923297_20-CA1R.CEL.gz 2.0 Mb (ftp)(http) CEL
Raw data provided as supplementary file
Processed data included within Sample table

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