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Sample GSM259454 Query DataSets for GSM259454
Status Public on Nov 29, 2008
Title dmpARC_LDvsSD_rep4
Sample type RNA
 
Channel 1
Source name Cy3-Short Day Photoperiod
Organism Phodopus sungorus
Characteristics 6 month old males were used for the study. The animals were maintained in short day photoperiod for 14 weeks before sacrifice. Brains were removed and sectioned. From the hypothalamic sections, dmpARC region was dissected using laser capture microdissection.
Biomaterial provider Rowett Research Institute
Extracted molecule polyA RNA
Extraction protocol Total RNA was extracted from the captured brain tissues. RNA was amplified using the reagents of aminoallyl Message amplification kit.
Label Cy3
Label protocol Using the regents in aminoallyl Message amplification kit and according to the instructions of the manufacturer (Ambion).
 
Channel 2
Source name Cy5-LongDay Photoperiod
Organism Phodopus sungorus
Characteristics 6 month old males were used for the study. The animals were maintained in long day photoperiod for 14 weeks before sacrifice. Brains were removed and sectioned. From the hypothalamic sections, dmpARC region was dissected using laser capture microdissection.
Biomaterial provider Rowett Research Institute
Extracted molecule polyA RNA
Extraction protocol Total RNA was extracted from the captured brain tissues. RNA was amplified using the reagents of aminoallyl Message amplification kit.
Label Cy5
Label protocol Using the regents in aminoallyl Message amplification kit and according to the instructions of the manufacturer (Ambion).
 
 
Hybridization protocol Hybridisation solution was prepared containing 130-160pmol of labelled RNA, 4ug of mouse Cot-1 DNA (Ambion, UK) and 3ul of 100x Denhardt’s solution made upto 130ul with Arrayhyb Microarray Hybridisation buffer (Sigma, UK). Prior to hybridisation, the microarray slides were prehybridised and placed in a GeneTAC hybridisation station (Genomic Solutions). The slides were heated to 55oC before addition of the hybridisation solution. The hybridisation was performed at 65oC for 16h, after which point the slides were washed with 0.5x SSC at 50oC for 3min, twice with 0.2x SSC/0.2% SDS at 50oC for 3min each and finally twice with 0.1x SSC at 20oC for 3min each.
Scan protocol Slides were scanned in two channels using a GeneTAC LS IV hybridisation station (Genomic solution). The signal intensities were measured using the GeneTAC Integrator version 3.0.1 software (Genomic solution).
Description Each sample comes from one individual animal (no pools were used).
Data processing Loess normalization was used to remove intensity depending dye-effects and also to transform intensities to the log2-scale. As each clone was spotted in triplicates on the array, we averaged across the three replicates to obtain one log-ratio value per array/pair of samples. Spots that had been flagged during the image analysis process were omitted in this averaging process.
 
Submission date Jan 25, 2008
Last update date Nov 29, 2008
Contact name Gill Campbell
E-mail(s) G.Campbell@abdn.ac.uk
Phone +44 (0) 1224 716627
Fax +44 (0) 1224 716647
URL http://www.rowett.ac.uk
Organization name University of Aberdeen
Department Rowett Institute of Nutrition and Health
Street address Greenburn Road
City Aberdeen
ZIP/Postal code AB21 9SB
Country United Kingdom
 
Platform ID GPL6150
Series (1)
GSE10278 Photoperiod regulates genes encoding melanocortin 3 and serotonin receptors, and secretogranins expressed in the dmpARC of the Siberian hamster

Data table header descriptions
ID_Ref
VALUE log2-ratio = log2(Cy5/Cy3)
log2(Cy3) log2-transformed Cy3 intensity
log2(Cy5) log2-transformed Cy5 intensity

Data table
ID_Ref VALUE log2(Cy3) log2(Cy5)
10I24 1.587361807 6.538683135 8.126044942
10E8 1.039963526 6.447677606 7.487641132
9A16 null null null
8M20 -0.836252276 5.86770277 5.031450494
8I4 -0.145935461 6.966696223 6.820760762
10M24 null null null
10I8 null null null
9E16 null null null
8A24 null null null
8M4 null null null
11A4 0.79459536 5.234301721 6.028897081
10M8 7.605758392 1.395503375 9.001261767
9I16 null null null
8E24 0.136851778 5.621181271 5.758033049
8A8 null null null
11E4 0.816601755 4.50514889 5.321750645
10A12 null null null
9M16 1.25782556 6.266212837 7.524038397
8I24 null null null
8E8 null null null

Total number of rows: 4045

Table truncated, full table size 111 Kbytes.




Supplementary file Size Download File type/resource
GSM259454.txt.gz 122.5 Kb (ftp)(http) TXT
Raw data provided as supplementary file
Processed data included within Sample table

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