NCBI Logo
GEO Logo
   NCBI > GEO > Accession DisplayHelp Not logged in | LoginHelp
GEO help: Mouse over screen elements for information.
          Go
Sample GSM834994 Query DataSets for GSM834994
Status Public on Jun 22, 2012
Title MSC_IL
Sample type RNA
 
Source name Mesenchymal stem cell, IL-1β
Organism Homo sapiens
Characteristics treatment: IL-1β for 24 hours at 37C
cell type: Mesenchymal stem cell
Treatment protocol Human bone marrow MSC were treated or not with IL-1β (25 ng/mL) for twenty four hours at 37 ºC in a humidified incubator with 5% CO2
Extracted molecule total RNA
Extraction protocol Total RNA was extracted from BM-MSC using the High Pure RNA Isolation kit (Roche) and was quantified by spectrometry (NanoDrop ND-1000, NanoDrop Technologies).
Label Cy3
Label protocol 800 ng of total RNA were used to produce Cyanine 3-CTP-labeled cRNA using the Low RNA Input Linear Amplification Kit, PLUS, One-Color (Agilent p/n 5188-5339) according to the manufacturer’s instructions.
 
Hybridization protocol Based on the protocol for One-Color Microarray-Based Gene Expression Analysis Version 5.5 (Agilent p/n 5188-5977), 3μg of labeled cRNA was hybridized with Whole Human Genome Oligo Microarray Kit (Agilent p/n G4112F) containing 41,000+ unique human genes and transcripts.
Scan protocol Arrays were scanned in an Agilent Microarray Scanner (Agilent G2565BA) according to the manufacturer’s protocol and data extracted using Agilent Feature Extraction Software 9.5.1 (http://www.chem.agilent.com/en-us/products/instruments/dnamicroarrays/featureextractionsoftware/pages/default.aspx).
Description Mesenchymal stem cell in response IL-1β
Data processing Signal was standardized across arrays using quantile normalization. Differential gene expression was carried out using the fold change. Gene set analysis was carried out for the Gene Ontology terms using FatiScan
 
Submission date Nov 16, 2011
Last update date Jun 22, 2012
Contact name Francisco García García
E-mail(s) fgarcia@cipf.es
Organization name CIPF
Department Bionformatics & Biostatistics Unit
Street address Eduardo Primo Yúfera, 3
City Valencia
ZIP/Postal code 46012
Country Spain
 
Platform ID GPL4133
Series (1)
GSE33755 Effect of IL-1β on mesenchymal stem cells

Data table header descriptions
ID_REF
VALUE processed Cy3 signal intensity (Agilent gProcessedSignal)

Data table
ID_REF VALUE
1 4.312896e+005
2 6.060519e+000
3 6.081402e+000
4 6.098772e+000
5 6.114686e+000
6 6.128341e+000
7 6.139239e+000
8 6.148996e+000
9 6.156965e+000
10 6.163728e+000
11 6.168003e+000
12 2.613919e+002
13 2.251725e+002
14 1.277253e+003
15 4.129362e+001
16 3.140251e+004
17 1.931151e+001
18 4.912401e+002
19 1.235169e+005
20 6.587343e+001

Total number of rows: 45015

Table truncated, full table size 868 Kbytes.




Supplementary file Size Download File type/resource
GSM834994_US45102947_251485034676_S01_GE1-v5_95_Feb07_1_2.txt.gz 8.9 Mb (ftp)(http) TXT
Processed data included within Sample table

| NLM | NIH | GEO Help | Disclaimer | Accessibility |
NCBI Home NCBI Search NCBI SiteMap