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Sample GSM690624 Query DataSets for GSM690624
Status Public on Feb 21, 2012
Title Short Day, 14 days (080212MJA_rat230-2.0_LRe16)
Sample type RNA
Source name Short Day, 14 days
Organism Rattus norvegicus
Characteristics strain: F344N
tissue: hypothalamic arcuate nucleus
protocol: Short 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_LRe16
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 9.540843106
113882_at 6.201729686
113892_at 17.7003562
113893_at 1568.709652
113894_at 1991.912371
113898_at 1499.38731
113900_at 81.4741247
113901_at 7.797009917
113902_at 23.09952423
113906_at 132.4218863
113907_at 3.457986523
113911_at 5.66553082
113912_at 11.13057751
113914_at 5.770430796
113917_at 34.42798502
113918_at 221.3177303
113922_at 2152.605678
113927_at 88.71323284
113929_at 172.0083506
113931_at 10.00588462

Total number of rows: 11498

Table truncated, full table size 242 Kbytes.

Supplementary file Size Download File type/resource
GSM690624.CEL.gz 2.8 Mb (ftp)(http) CEL
Raw data provided as supplementary file
Processed data included within Sample table

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