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Sample GSM994726 Query DataSets for GSM994726
Status Public on Sep 12, 2013
Title Islets Nkx6.1 Mutant B
Sample type RNA
 
Source name Isolated islets, mutant mice, pooled sample 2
Organism Mus musculus
Characteristics strain: Nkx6.1-flox [mixed FVB/N x C57Bl/6J] X Pdx1-CreERTM [mixed Cd1 X C57Bl/6J background]
tissue: Pancreatic islets
gender: male
age: 6 weeks
treatment: Tamoxifen
genotype: Nkx6.1fl/-;Pdx1-CreERTM Mutant
Treatment protocol Male mice were injected with 2 mg/25 g tamoxifen in corn oil four times between 4 and 6 weeks of age.
Growth protocol All animal experiments described herein were approved by the University of California, Irvine and San Diego Institutional Animal Care and Use Committees.
Extracted molecule total RNA
Extraction protocol Islets were isolated and stored in 350 μl of RLT lysis buffer (QIAGEN, Valencia, CA) in the –80°C freezer. Each individual RNA sample was collected from two pancreata of the same genotype as per the manufacturer's instructions. We prepared RNA samples in ~12 μl of RNase free water. RNA was quantified using a NanoDrop-1000 spectrophotometer and quality was monitored with the Agilent 2100 Bioanalyzer (Agilent Technologies, Santa Clara, CA).
Label Cy3
Label protocol QuickAmp Low Input labelling: 150 ng total RNA labeled with Cy3. Specific Activity of > 6 pmol dye/µg cRNA accepted.
 
Hybridization protocol Standard Agilent hybridization with 1650 ng cRNA. 17-19 hrs @ 65°C. Standard Agilent wash including Stabilization & Drying Solution.
Scan protocol Model G2505B Agilent Scanner. One color. 100% and 10% PMT settings for Extended Dynamic Range. 5µm resolution.
Description Gene expression of islets at 6 weeks of age after deletion of Nkx6.1
Data processing Raw Data extraction using Agilent Feature Extraction Software v10.7.3.1 using protocol GE1_107_Sep09 . Normalization, a modified LOESS.
 
Submission date Aug 29, 2012
Last update date Sep 12, 2013
Contact name Brandon Taylor
Organization name University of California, San Diego
Department Pediatrics and Cellular & Molecular Medicine
Lab Maike Sander, M.D.
Street address Sanford Consortium for Regenerative Medicine, 2880 Torrey Pines Scenic Dr., Room 3101
City La Jolla
State/province CA
ZIP/Postal code 92037
Country USA
 
Platform ID GPL10333
Series (1)
GSE40470 Identification of Nkx6.1 regulated genes in mature pancreatic islets.

Data table header descriptions
ID_REF
VALUE Normalized signal intensity

Data table
ID_REF VALUE
12 201.7
13 58.5
14 1763.6
15 88
16 4669.3
17 4814.9
18 211
19 61.9
20 80
21 209.2
22 578.9
23 75995.4
24 858.4
25 1908.6
26 642.2
27 6410.4
28 1778.2
30 5043.2
31 5888.2
32 54.1

Total number of rows: 43020

Table truncated, full table size 490 Kbytes.




Supplementary file Size Download File type/resource
GSM994726_US22502657_252665511831_S01_GE1_107_Sep09_1_2.txt.gz 9.1 Mb (ftp)(http) TXT
Processed data included within Sample table
Processed data provided as supplementary file

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