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Sample GSM690623 Query DataSets for GSM690623
Status Public on Feb 21, 2012
Title Long Day, 14 days (080212MJA_rat230-2.0_LRe15)
Sample type RNA
Source name Long Day, 14 days
Organism Rattus norvegicus
Characteristics strain: F344N
tissue: hypothalamic arcuate nucleus
protocol: Long Day
time: 14 days
Extracted molecule total RNA
Extraction protocol Total RNA was extracted from the arcuate nucleus tissue using an RNeasy Mini Kit (Qiagen, UK) following the manufacturer's instructions. The RNA, whilst on the RNeasy columns, was treated with DNase1 (Qiagen, UK) and washed following the manufacturer's instructions.
Label biotin
Label protocol 2 μg of high quality total RNA, verified using the RNA 6000 Nano assay on the Agilent 2100 Bioanalyzer (Agilent Technologies), was used with the Affymetrix Eukaryotic One-Cylce Target Labeling and Control reagents (#900493) following the manufacturers instructions to generate Biotin-labeled antisense cRNA.
Hybridization protocol The labeled and fragmented cRNA (10ug) was used for the hybridization to the Affymetrix Rat 230 2.0 Genome Genechips for 16 hr at 45C. An automated process of washing and staining in the Affymetrix Fluidics Station 400 was performed.
Scan protocol Affymetrix arrays were scanned using the Affymetrix 3000G scanner. Absolute values of expression were calculated from the scanned array using the Affymetrix Command Console v1 software.
Description 080212MJA_rat230-2.0_LRe15
Data processing CEL files were transferred to MadMax website (, and data analysis was performed using the statistical programming language R and the R libraries offered by the Bioconductor project. The data were first explored for quality control purposes and were normalized the GCRMA method within Bioconductor. We employed an updated and remapped mapping of Probes to Entrez Gene IDs as implemented in the R package rat2302rnentrezgcdf (v10.0.0).
Submission date Mar 14, 2011
Last update date Feb 21, 2012
Contact name Alexander W Ross
Organization name University of Aberdeen Rowett Institute of Nutrition and Health
Department Obesity and Metabolic Health
Lab Molecular Neuroendocrinology
Street address Greenburn Road, Bucksburn
City Aberdeen
State/province Scotland
ZIP/Postal code AB21 9SB
Country United Kingdom
Platform ID GPL8201
Series (1)
GSE27926 Expression data from F344N rats in long and short photoperiods

Data table header descriptions
VALUE GCRMA normalised intensities on the original (unlogged) scale

Data table
112400_at 8.568660189
113882_at 5.474920169
113892_at 18.3397518
113893_at 1596.46619
113894_at 1987.07341
113898_at 1722.874293
113900_at 56.42700755
113901_at 8.025973232
113902_at 34.51220875
113906_at 71.6864047
113907_at 3.866814369
113911_at 7.018418051
113912_at 12.73796239
113914_at 5.370439441
113917_at 38.75001817
113918_at 111.1700428
113922_at 2007.176575
113927_at 48.48292656
113929_at 140.3591901
113931_at 8.234841403

Total number of rows: 11498

Table truncated, full table size 242 Kbytes.

Supplementary file Size Download File type/resource
GSM690623.CEL.gz 2.7 Mb (ftp)(http) CEL
Raw data provided as supplementary file
Processed data included within Sample table

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