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Sample GSM400829 Query DataSets for GSM400829
Status Public on Jan 01, 2010
Title Tadpole pancreas 62-Pan#3
Sample type RNA
 
Channel 1
Source name Tadpole, pancreas, NF62
Organism Xenopus laevis
Characteristics development stage: tadpole [Nieuwkoop and Faber stage (NF) 62]
tissue: pancreas
individual identifier: 251321410051
agent: Thyroid Hormone (TH)
Biomaterial provider Donald Brown,Carnegie Institution,3520 San Martin Dr,Baltimore,MD,21218 E-mail: brown@ciwemb.edu
Treatment protocol Xenopus tadpoles (NF52, NF62, and NF66) were euthanized with ice-cold MS222, excess water was blotted from the animals with tissue paper, small incision was made on the belly for quick fixation and samples were fixed in RNA-Later overnight at 4C and used for RNA extraction in TRIZOL reagent. Pancreas and liver from 5-10 tadpoles were pooled together as one replicate and there were three replicates at each time of exposure.
Extracted molecule total RNA
Extraction protocol TRIZOL standard extraction method was used . The full protocol can be found in the Life Technologies CAT 15596. Homogenize tissue samples in 1 mL of TRIZOL reagent per 50-100 mg of tissue using 1.5 Pellet Pestile (Nalge Nunc International). The sample volume should not exceed 10% of the volume of TRIZOL Reagent used for homogenization. Incubate the homogenized samples for 5 minutes at room temperature to permit the complete dissociation of nucleoprotein complexes. Add 0.2 mL of chloroform per 1 mL of TRIZOL Reagent. Cap sample tubes securely. Shake tubes vigorously by hand for 15 seconds and incubate them at room temperature for 2 to 3 minutes. Centrifuge the samples at no more than 12,000 x g for 15 minutes at 4 degree. Following centrifugation, the mixture separates into a lower red, phenol-chloroform phase, an interphase, and a colorless upper aqueous phase. RNA remains exclusively in the aqueous phase. The volume of the aqueous phase is about 60% of the volume of TRIZOL Reagent used for homogenization. Transfer the aqueous phase to a fresh tube, and precipitate the RNA from the aqueous phase by mixing with isopropyl alcohol. Use 0.5 mL of isopropyl alcohol per 1 mL of TRIZOL Reagent used for the initial homogenization. Incubate samples at room temperature for 10 minutes and centrifuge at no more than 12,000 x g for 10 minutes at 4 degree. The RNA precipitate, often invisible before centrifugation, forms a gel-like pellet on the side and bottom of the tube. Remove the supernate. Wash the RNA pellet once with 75% ethanol, adding at least 1 mL of 75% ethanol per 1 mL of TRIZOL Reagent used for the initial homogenization. Mix the sample by vortexing and centrifuge at no more than 7,500 x g for 5 minutes at 4 degree. Redissolving the RNA at the end of procedure, briefly drying the RNA pellet.
Label Cy3
Label protocol Total RNA was labeled using Agilents Fluorescent Linear Amplification kit, according to manufacturers instructions (Product Number G2554A or P/N G2556-66002, Version 3.0, June 2002).
 
Channel 2
Source name Universal RNA
Organism Xenopus laevis
Characteristics reference: Universal Xenopus Laevis Reference RNA
Extracted molecule total RNA
Extraction protocol mRNAs were extracted with QuickPrep Micro mRNA Purification Kit from Amersham
Label Cy5
Label protocol Total RNA was labeled using Agilents Fluorescent Linear Amplification kit, according to manufacturers instructions (Product Number G2554A or P/N G2556-66002, Version 3.0, June 2002).
 
 
Hybridization protocol Agilent 60-mer oligo microarray processing protocol (SSC Wash/SureHyb Chamber set-up) V4.1, April 2004. Agilent Publication Number: G4140-90030 V4.1 APRIL 2004.
Scan protocol Slides were scanned with an Agilent DNA Microarray Scanner (model G2505-64120) at 100% and 10% PMT in both channels, with a scan resolution of 5um.
Description 62-Pan
Data processing Data are extracted with Agilent Feature Extraction Software.The data were further processed with NIA ANOVA tool utilities.See http://lgsun.grc.nia.nih.gov/ANOVA for details.
The data is normalized with the following method:
(1) Take values from the columns gDyeNormSignal,rDyeNormSignal in the raw files and log-transform them using: log10(max(x,1)). These values will be referenced below as Xgi and Xri where i is array number.
(2) Take average of Xri's for the oligo among 9 arrays in the series: AverXr = average(Xri).
(3) For each array estimate Yi = Xgi-Xri+AverXr
(4) Round Yi to 4 decimal digits. This is used as the normalized VALUE.
More detailed information with error correction can be found at http://lgsun.grc.nia.nih.gov/ANOVA/help.html#arrayjoin
 
Submission date May 07, 2009
Last update date May 18, 2009
Contact name Donald Brown
E-mail(s) brown@ciwemb.edu
Organization name Carnegie Institution
Department Department of Embryology
Street address 3520 San Martin Dr
City Baltimore
State/province MD
ZIP/Postal code 21218
Country USA
 
Platform ID GPL3936
Series (2)
GSE16018 Thyroid Hormone (TH) Controls The Remodeling Of The Pancreas And The Liver, Part C
GSE16075 Thyroid Hormone (TH) Controls The Remodeling Of The Pancreas And The Liver

Data table header descriptions
ID_REF Feature Number (FeatureNum). Please check the platform file for the annotation.
VALUE The normalized value described in the Data Processing section.

Data table
ID_REF VALUE
3 2.6391
4 2.3078
5 2.8792
8 2.6941
9 1.9561
10 3.4005
11 2.5301
12 2.2638
13 2.0990
15 2.5817
16 3.7402
17 2.2893
18 2.5105
19 2.5743
20 1.9813
22 2.3872
23 1.8729
24 2.7549
25 2.2752
26 2.1799

Total number of rows: 21495

Table truncated, full table size 262 Kbytes.




Supplementary file Size Download File type/resource
GSM400829.txt.gz 5.2 Mb (ftp)(http) TXT
Processed data included within Sample table

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