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Sample GSM563350 Query DataSets for GSM563350
Status Public on Mar 17, 2011
Title Footpads_M. leprae infected_12 month_rep6
Sample type RNA
 
Channel 1
Source name M. lepare non-infected footpads
Organism Mus musculus
Characteristics tissue: footpads
strain: CAnN.Cg-Foxn1nu/CrljBgi
experimental period: 12 months
Treatment protocol M. leprae non-infected footpads: PBS (subcutaneous injection), M. leprae-infected footpads: 2´10^6 bacteria (subcutaneous injection)
Extracted molecule total RNA
Extraction protocol (1) Total RNA extracted using Trizol following manufacturer's instructions, (2) DNA removal using Rneasy RNA extraction column following manufacturer's instructions
Label Cy3
Label protocol Direct Labeling (20 µg of total RNA were primed with oligo dT(18) primer at 70°C for 10 min, then reversed transcribed at 42°C for 1 h in the presence of Reverse transcriptase, and dNTP, cyanine dCTP (control - Cy3 and sample-Cy5)
Labeled cDNA were purifed with 3M sodium acetate and absoulte ethanol, checked quality of synthesized labeled-cDNA (Spectrophotometer A260, A650, A550), and the calculated concentration and incorporation rate
 
Channel 2
Source name M. lepare-infected footpads
Organism Mus musculus
Characteristics tissue: footpads
strain: CAnN.Cg-Foxn1nu/CrljBgi
period: 12 months
Treatment protocol M. leprae non-infected footpads: PBS (subcutaneous injection), M. leprae-infected footpads: 2´10^6 bacteria (subcutaneous injection)
Extracted molecule total RNA
Extraction protocol (1) Total RNA extracted using Trizol following manufacturer's instructions, (2) DNA removal using Rneasy RNA extraction column following manufacturer's instructions
Label Cy5
Label protocol Direct Labeling (20 µg of total RNA were primed with oligo dT(18) primer at 70°C for 10 min, then reversed transcribed at 42°C for 1 h in the presence of Reverse transcriptase, and dNTP, cyanine dCTP (control - Cy3 and sample-Cy5)
Labeled cDNA were purifed with 3M sodium acetate and absoulte ethanol, checked quality of synthesized labeled-cDNA (Spectrophotometer A260, A650, A550), and the calculated concentration and incorporation rate
 
 
Hybridization protocol Purifed cDNA were denatured, and the samples were applied to microarrays enclosed in hybridization chambers. After hybridization, slides were washed sequential ((1) 2XSSC, 0.1%SDS, (2) 1XSSC, (3) 0.2XSSC) and were dried by centrifuge
Scan protocol Scanned on an Genepix 4000B scanner.
Images were quantified using GenePix pro Software (version 5.1).
Description Footpads_M. leprae infected_12 month_rep6
Data processing Box plot and Intesity dependent (LOWESS) normalized, background subtracted data obtained from log2 of processed Red signal/processed Green signal. GenePix pro 5.1 was used.
 
Submission date Jul 07, 2010
Last update date Mar 17, 2011
Contact name Tae Hoon Kim
E-mail(s) ecotype531@catholic.ac.kr
Phone 82-2-2258-7451
Fax 82-2595-2241
URL http://www.hansen.re.kr
Organization name Medical College of the Catholic University
Department Pathology
Lab Institute of Hansen's Disease
Street address 505 Bonpo-dong
City Seoul
State/province Socho-gu
ZIP/Postal code 138-701
Country South Korea
 
Platform ID GPL10650
Series (1)
GSE22784 Profiling of Gene expression in Mycobacterium leprae (M. leprae)-infected footpad of BALB/c nu/nu mice

Data table header descriptions
ID_REF
VALUE normalized log2 ratio (Cy5/Cy3) representing sample/control

Data table
ID_REF VALUE
1
2 -0.131715069
3 0.317845709
4
5
6 -0.764943999
7 -0.642024332
8 -0.704096851
9 -0.506586542
10 1.510462576
11 -1.378305226
12 -1.195122866
13 -1.173923996
14
15
16 -0.262216877
17 -0.307374485
18 -0.294543338
19 -0.467405365
20 -0.46391251

Total number of rows: 37440

Table truncated, full table size 570 Kbytes.




Supplementary file Size Download File type/resource
GSM563350.txt.gz 2.8 Mb (ftp)(http) TXT
Processed data included within Sample table

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