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Sample GSM206009 Query DataSets for GSM206009
Status Public on Jun 27, 2007
Title hypothalamus of juvenile (JUV) rat_JUV2
Sample type RNA
 
Source name Hypothalamus of 26 day old juvenile female rat
Organism Rattus norvegicus
Characteristics Hypothalamus of 26 day old female juvenile rat
Biomaterial provider Tissue samples were obtained from normal female Sprague Dowley rats.
Treatment protocol Tissue was rapidly extracted and stored in RNAlater solution (Ambion) according to the manufacturers instructions.
Growth protocol none
Extracted molecule total RNA
Extraction protocol Total RNA was isolated and purified using RNeasy Mini Columns according to the manufacturer’s specifications. RNA quality was assessed by OD reading and was subjected to electrophoretic trace using an Agilent Bioanalyzer (Agilent Technologies, Palo Alto, CA).
Label Biotin
Label protocol For target labelling, messenger RNA was amplified and labeled from 2 mg of total RNA in two steps. In the first step, mRNA was converted to double-stranded cDNA using Superscript Reverse Transcriptase (Invitrogen) and an oligo-dT primer linked to a T7 RNA polymerase binding site sequence (IDT). In the second step, amplified and labeled cRNA (the target) was produced in an in vitro transcription reaction using T7 RNA polymerase and biotin-UTP (Affymetrix, Santa Clara, CA). Following removal of free nucleotides, target yield was measured by UV260 absorbance. For target quality assessment, approximately 200 ng of each sample cRNA target along with a control cRNA target was analyzed on the RNA 6000 LabChip using the 2100 Bioanalyzer (Agilent). The target quality was determined based on yield and cRNA size distribution produced in the in vitro synthesis reaction. Samples that fail quality control were discarded or relabeled.
 
Hybridization protocol For array hybridization and processing, the labelled target was fragmented at 95°C in the presence of high magnesium concentration. The fragmented material was combined with biotinylated hybridization control oligomer and biotinylated control cRNAs for BioB, BioC, BioD and cre (Affymetrix) in hybridization buffer. Ten mg of target was hybridized with the GeneChip (Rat Genome 230 2.0) array (Affymetrix) overnight, followed by washing, staining, signal amplification with biotinylated anti-streptavidin antibody, and a final staining step on the Fluidics Station (Affymetrix). The distribution of fluorescent material on the processed array was determined using the GeneArray laser scanner (Affymetrix). Image inspection was performed manually immediately following each scan.
Scan protocol The array image scan was processed with Affymetrix Microarray Suite software, version 5.0 (MAS 5.0). The GeneChip expression arrays contained control probe sets for both spiked and endogenous RNA transcripts (e.g., BioB, BioC, BioD, cre and species-specific actin and GAPDH).
Description gene expression data derived from a hypothalamus of a normal juvenile female rat. This sample is considered as a control sample.
Data processing Image processing and expression analysis were performed using Affymetrix Microarray Suite (MAS) 5.0 software. An absolute (single assay) expression analysis was performed for each GeneChip genome array hybridization. The GeneChip expression arrays contain control probe sets for both spiked and endogenous RNA transcripts (e.g., BioB, BioC, BioD, CreX and species-specific actin and GAPDH). Following image processing and absolute analysis of the array pattern with MAS 5.0, six parameters were examined to assess the overall assay performance: background, noise, average signal, % present, ratio of signal values for probe sets representing the 5’ and 3’ ends of actin and GAPDH transcripts, and total signal for BioC, BioD and CreX probe sets. Prior to further analysis, array data were globally scaled to a uniform, average target intensity for all assays prior to further analysis. Initial filters removed all absent genes and genes with no change across all data sets.
 
Submission date Jun 27, 2007
Last update date Aug 14, 2011
Contact name Alejandro Lomniczi
E-mail(s) lomniczi@ohsu.edu
Phone 503-690-5305
Fax 503-690-5384
Organization name Oregon National Primate Research Center - OHSU
Department Neuroscience
Street address 505 NW 185th Ave
City Beaverton
State/province OR
ZIP/Postal code 97006
Country USA
 
Platform ID GPL1355
Series (1)
GSE8310 Gene expression data from hypothalamus of normal sexual development of the female rat

Data table header descriptions
ID_REF
VALUE MAS5.0-calculated signal intensity
ABS_CALL indicating whether the transcript was present (P), absent (A), or marginal (M)
DETECTION P-VALUE

Data table
ID_REF VALUE ABS_CALL DETECTION P-VALUE
AFFX-BioB-5_at 146.421 P 0.0125468
AFFX-BioB-M_at 141.454 P 0.000753643
AFFX-BioB-3_at 116.617 P 0.00556451
AFFX-BioC-5_at 436.205 P 0.000296708
AFFX-BioC-3_at 434.198 P 9.4506e-05
AFFX-BioDn-5_at 802.904 P 9.4506e-05
AFFX-BioDn-3_at 1558.07 P 0.000169227
AFFX-CreX-5_at 3902.93 P 5.16732e-05
AFFX-CreX-3_at 4991.54 P 4.42873e-05
AFFX-DapX-5_at 2.55868 A 0.804734
AFFX-DapX-M_at 31.4027 A 0.123572
AFFX-DapX-3_at 4.89872 A 0.824672
AFFX-LysX-5_at 1.72861 A 0.672921
AFFX-LysX-M_at 23.7761 A 0.354453
AFFX-LysX-3_at 4.20984 A 0.216524
AFFX-PheX-5_at 1.77932 A 0.712257
AFFX-PheX-M_at 5.28526 A 0.891021
AFFX-PheX-3_at 11.1312 A 0.814869
AFFX-ThrX-5_at 5.3234 A 0.921998
AFFX-ThrX-M_at 21.2156 A 0.559354

Total number of rows: 31099

Table truncated, full table size 947 Kbytes.




Supplementary file Size Download File type/resource
GSM206009.CEL.gz 2.9 Mb (ftp)(http) CEL
GSM206009.CHP.gz 165.1 Kb (ftp)(http) CHP
Raw data provided as supplementary file
Processed data included within Sample table
Processed data provided as supplementary file

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