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Sample GSM1046968 Query DataSets for GSM1046968
Status Public on Nov 30, 2012
Title Contol6 ZP38 mRNA
Sample type RNA
 
Source name Contol6 ZP38
Organism Homo sapiens
Characteristics cell type: dermal mesenchymal stem cell
age: 44 years
gender: male
pasi: ——
Growth protocol The dermises were separated from the epidermis by dispase and monoplast suspension was obtained by pipetting. The MSCs were cultured by adherent assay. Cells of 3rd passage were enrolled in the microarry.
Extracted molecule total RNA
Extraction protocol Total RNA was isolated using TRIzol (Invitrogen) and miRNeasy mini kit (QIAGEN) according to manufacturer’s instructions, which efficiently recovered all RNA species, including miRNAs. RNA quality and quantity was measured by using nanodrop spectrophotometer (ND-1000, Nanodrop Technologies) and RNA Integrity was determined by gel electrophoresis
Label Cy3
Label protocol 1 μg of total RNA from each sample was linearly amplified and labeled with Cy3-dCTP. The Labeled cRNAs were purified by RNAeasy Mini Kit (Qiagen). The concentration and specific activity of the labeled cRNAs (pmol Cy3/μg cRNA) were measured by NanoDrop ND-1000. 1μg of each labeled cRNA was fragmented by adding 11 μl 10 × Blocking Agent and 2.2 μl of 25×Fragmentation Buffer, then heated at 60 °C for 30 min, and finally 55 μl 2 × GE Hybridization buffer was added to dilute the labeled cRNA
 
Hybridization protocol 100μl of hybridization solution was dispensed into the gasket slide and assembled to the gene expression microarray slide. The slides were incubated for 17 hours at 65°C in an Agilent Hybridization Oven. The hybridized arrays were washed, fixed and scanned with using the Agilent DNA Microarray Scanner (part number G2505B).
Scan protocol scanned with using the Agilent DNA Microarray Scanner (part number G2505B).
Data processing Agilent Feature Extraction software (version 10.7.3.1) was used to analyze the acquired array images. Quantile normalization and subsequent data processing were performed with using the GeneSpring GX v11.5.1 software package (Agilent Technologies). After quantile normalization of the raw data, genes that at least 4 out of 12 samples have flags in Detected (“All Targets Value”) were chosen for further data analysis. Differentially expressed genes were identified through volcano plot filtering. Hierarchical Clustering was performed using the Agilent GeneSpring GX software (version 11.5.1). GO analysis and Pathway analysis were performed in the standard enrichment computation method
 
Submission date Nov 29, 2012
Last update date Nov 30, 2012
Contact name Ruixia Hou
E-mail(s) hrx0205@163.com
Organization name Taiyuan City Central Hospital
Department Dermatology
Street address 1,Dong San Dao Xiang, Jiefang Road
City Taiyuan
State/province Shanxi
ZIP/Postal code 030009
Country China
 
Platform ID GPL13497
Series (1)
GSE42632 mRNA expression profile of dermal MSCs derived from psoriasis patients and normal control

Data table header descriptions
ID_REF
VALUE Normalized signal intensity

Data table
ID_REF VALUE
A_23_P42935 7.6656528
A_23_P117082 12.7522545
A_23_P2683 9.470964
A_33_P3367647 6.6666765
A_23_P157316 6.8208284
A_32_P14850 14.956677
A_23_P158596 7.7601967
A_23_P350107 8.700623
A_23_P388190 9.1043825
A_23_P106544 10.602267
A_32_P85539 9.612454
A_23_P94998 8.090635
A_23_P417014 4.1329465
A_23_P103905 10.202939
A_24_P497186 8.903805
A_23_P118536 8.493961
A_23_P434289 7.2481084
A_33_P3326898 5.7452908
A_24_P67898 11.013213
A_24_P28657 8.818452

Total number of rows: 28908

Table truncated, full table size 640 Kbytes.




Supplementary file Size Download File type/resource
GSM1046968_ZP38.txt.gz 2.1 Mb (ftp)(http) TXT
Processed data included within Sample table

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