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Sample GSM836206 Query DataSets for GSM836206
Status Public on Nov 19, 2011
Title MSC from patient B256
Sample type RNA
 
Channel 1
Source name MSC from pediatric patient B256
Organism Homo sapiens
Characteristics cell type: mesenchymal stem cell (MSC)
disease state: pediatric severe aplastic anemia (SAA)
patient identifier: B256
Treatment protocol Patients who had appropriate donors were having a bone transplantation; otherwise, they received anti-thymocyte immunoglobulins.
Growth protocol Mesenchymal stem cells (MSCs) were kept in an undifferentiated, pluripotent state by growing in DMEM with low glucose concentration.
Extracted molecule total RNA
Extraction protocol Total RNA was extracted using Trizol following the manufacturer's instructions.
Label Cy5
Label protocol cRNA was synthesized from 0.5 μg of total RNA, and the RNA was amplified (Fluorescent Linear Amplification Kit, Agilent Technologies, Santa Clara, CA) and labeled with Cy3-CTP or Cy5-CTP (PerkinElmer, Waltham, MA). The cRNA of MSC from SAA patients was labeled with Cy5 and the cRNA from the control group was labeled with Cy3. The Cy-labeled cRNA was fragmented to about 50-100 nucleotides long by incubation with fragmentation buffer (Agilent Technologies, Santa Clara, CA) at 60°C for 30 minutes.
 
Channel 2
Source name Pooled MSC from healthy donors
Organism Homo sapiens
Characteristics cell type: mesenchymal stem cell (MSC)
disease state: healthy
sample type: reference
Treatment protocol Patients who had appropriate donors were having a bone transplantation; otherwise, they received anti-thymocyte immunoglobulins.
Growth protocol Mesenchymal stem cells (MSCs) were kept in an undifferentiated, pluripotent state by growing in DMEM with low glucose concentration.
Extracted molecule total RNA
Extraction protocol Total RNA was extracted using Trizol following the manufacturer's instructions.
Label Cy3
Label protocol cRNA was synthesized from 0.5 μg of total RNA, and the RNA was amplified (Fluorescent Linear Amplification Kit, Agilent Technologies, Santa Clara, CA) and labeled with Cy3-CTP or Cy5-CTP (PerkinElmer, Waltham, MA). The cRNA of MSC from SAA patients was labeled with Cy5 and the cRNA from the control group was labeled with Cy3. The Cy-labeled cRNA was fragmented to about 50-100 nucleotides long by incubation with fragmentation buffer (Agilent Technologies, Santa Clara, CA) at 60°C for 30 minutes.
 
 
Hybridization protocol The fragmented Cy-labeled cRNA was pooled, and oligoarray control targets and hybridization buffer (Agilent In Situ Hybridization Kit Plus) were added. The samples were applied to Agilent Whole Human Genome 4x44k oligo microarrays (Agilent Technologies, Santa Clara, CA) enclosed in Agilent SureHyb-enabled hybridization chambers and hybridized at 60°C for 17 h. After hybridization, slides were washed sequentially to remove non-specifically binding residues.
Scan protocol The hybridized microarrays were scanned with an Agilent microarray scanner (Agilent Technologies, Santa Clara, CA) at OD535 for Cy3 and OD625 for Cy5.
Description SAA B256
MSC from pediatric SAA patient vs. pooled MSC from healthy donors.
Data processing Scanned images were analyzed by Feature extraction software 8.1 (Agilent Technologies, Santa Clara, CA). After image analysis, the data were normalized by a rank-consistency-filtering LOWESS method, which was included in the package software of Feature extraction software 10.5.1.1 (Agilent Technologies, Santa Clara, CA).
 
Submission date Nov 18, 2011
Last update date Nov 21, 2011
Contact name Kuan-Chih Chow
E-mail(s) kcchow@dragon.nchu.edu.tw
Phone +886-4-22840896-118
Fax +886-4-22859270
Organization name National Chung Hsing University
Department Graduate Institute of Biomedical Sciences
Lab Cancer Research Lab.
Street address 250 Kuo Kuang Road
City Taichung
ZIP/Postal code 40227
Country Taiwan
 
Platform ID GPL4133
Series (1)
GSE33812 Gene expression profiles of bone marrow mesenchymal stem cells in pediatric patients with severe aplastic anemia

Data table header descriptions
ID_REF
VALUE Normalized log2 ratio (Cy5/Cy3) representing test/reference

Data table
ID_REF VALUE
1 0.091
2 0.000
3 0.000
4 0.000
5 0.000
6 0.000
7 0.000
8 0.000
9 0.000
10 0.000
11 0.000
12 -2.025
13 -0.814
14 -0.269
15 -0.257
16 0.027
17 0.433
18 -0.286
19 0.287
20 -0.387

Total number of rows: 45015

Table truncated, full table size 535 Kbytes.




Supplementary file Size Download File type/resource
GSM836206.txt.gz 7.6 Mb (ftp)(http) TXT
Processed data included within Sample table
Processed data are available on Series record

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