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Sample GSM1002259 Query DataSets for GSM1002259
Status Public on Sep 13, 2012
Title X1C
Sample type RNA
 
Source name C.elegans crh-1mutant
Organism Caenorhabditis elegans
Characteristics developmental stage: L4
genotype/variation: crh-1 mutant
Growth protocol C. elegans wild-type, kin-1(ok338)mutant and crh-1(tz2) mutant were grown to L4 at 20°C in NGM media. Then they infected 24 hours by fungi Drechmeria coniospora respectively.
Extracted molecule total RNA
Extraction protocol Total RNA from each sample was quantified by the NanoDrop ND-1000 and RNA integrity was assessed by standard denaturing agarose gel electrophoresis. About 5 μg total RNA of each sample was used for labeling and array hybridization as the following steps: 1) Reverse transcription with by Invitrogen Superscript ds-cDNA synthesis kit; 2) ds-cDNA labeling with NimbleGen one-color DNA labeling kit.
Label Cy3
Label protocol NimbleGen One-Color DNA Labeling Kit was used for sample labeling.
 
Hybridization protocol Array hybridization using the NimbleGen Hybridization System and followed by washing with the NimbleGen wash buffer kit.
Scan protocol Array scanning using the Axon GenePix 4000B microarray scanner (Molecular Devices Corporation).
Description This sample is of C.elegans crh-1(tz2) loss of function mutant. It is the first of three mutant strain biological replicates used in this experiment, each from separate cultures.
Data processing Scanned images (TIFF format) were then imported into NimbleScan software (version 2.5) for grid alignment and expression data analysis. Expression data were normalized through quantile normalization and the Robust Multichip Average (RMA) algorithm included in the NimbleScan software. The Probe level (*_norm_RMA.pair) files and Gene level (*_RMA.calls) files were generated after normalization. All gene level files were imported into Agilent GeneSpring GX software (version 11.5.1) for further analysis.
 
Submission date Sep 12, 2012
Last update date Sep 13, 2012
Contact name Cheng Gang Zou
E-mail(s) fushu111@qq.com
Phone +86 871 5031092
Fax +86 871 5034838
Organization name Yunnan University
Lab Laboratory for Conservation and Utilization of Bioresources
Street address No. 2,North of Cuihu Road
City Kunming
State/province Yunnan
ZIP/Postal code 650091
Country China
 
Platform ID GPL16046
Series (1)
GSE40809 Expression analysis of C. elegans genes kin-1 and crh-1 mutant

Data table header descriptions
ID_REF
VALUE Raw signal intensities were normalized in RMA method by NimbleScan v2.5, low intensity genes were filtered. Values are from *_RMA.calls files

Data table
ID_REF VALUE
WBGene00000001_aap_1_Y110A7A_10 2778.1118
WBGene00000002_aat_1_F27C8_1 1884.8235
WBGene00000003_aat_2_F07C3_7 792.9779
WBGene00000004_aat_3_F52H2_2 1098.6562
WBGene00000005_aat_4_T13A10_10 458.47104
WBGene00000006_aat_5_C55C2_5a 2849.7031
WBGene00000006_aat_5_C55C2_5b 3576.3865
WBGene00000006_aat_5_C55C2_5c 2837.2617
WBGene00000007_aat_6_T11F9_4a 777.7156
WBGene00000007_aat_6_T11F9_4b 773.7518
WBGene00000009_aat_8_F28F9_4 369.2731
WBGene00000010_aat_9_Y53H1C_1a 1363.631
WBGene00000010_aat_9_Y53H1C_1b 2162.0156
WBGene00000015_abf_4_Y38H6C_22 320.27997
WBGene00000016_abf_5_T22H6_5 739.5101
WBGene00000017_abf_6_T22H6_7 668.19867
WBGene00000018_abl_1_M79_1a 1133.9651
WBGene00000018_abl_1_M79_1b 1184.253
WBGene00000019_abt_1_C24F3_5 245.60043
WBGene00000020_abt_2_F12B6_1 1262.9141

Total number of rows: 15405

Table truncated, full table size 621 Kbytes.




Supplementary file Size Download File type/resource
GSM1002259_X1C_532.pair.gz 2.3 Mb (ftp)(http) PAIR
GSM1002259_X1C_532_norm_RMA.pair.txt.gz 2.3 Mb (ftp)(http) TXT
Processed data included within Sample table
Processed data provided as supplementary file
Processed data are available on Series record
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