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Sample GSM4910781 Query DataSets for GSM4910781
Status Public on Nov 18, 2020
Title Ta-modified Ti surface rep3
Sample type RNA
 
Source name marrow of rat tibias
Organism Rattus norvegicus
Characteristics cell type: rBMSCs
culture: Ta-modified Ti surface
Treatment protocol rBMSCs were isolated from the marrow of rat tibias, cells were cultured on Ta-modified surface for 7 days, gene expression in rBMSCs was measured.
Extracted molecule total RNA
Extraction protocol Total RNA was extracted using TRIZOL Reagent (Cat#15596-018,Life technologies, Carlsbad, CA, US) following the manufacturer’s instructions and checked for a RIN number to inspect RNA integrity by an Agilent Bioanalyzer 2100 (Agilent technologies, Santa Clara, CA, US). Qualified total RNA was further purified by NucleoSpin RNA Clean-up XS kit (Cat#740903, MN, Germany) and RNase-Free DNase Set (Cat#79254, QIAGEN, GmBH, Germany).
Label Cy3
Label protocol Total RNA was amplified and labeled by Low Input Quick Amp Labeling Kit, One-Color (Cat.# 5190-2305, Agilent technologies, Santa Clara, CA, US), following the manufacturer’s instructions. Labeled cRNA were purified by RNeasy mini kit (Cat.# 74106, QIAGEN, GmBH, Germany).
 
Hybridization protocol Each slide was hybridized with 600ng Cy3-labeled cRNA using Gene Expression Hybridization Kit (Cat.# 5188-5242, Agilent technologies, Santa Clara, CA, US) in Hybridization Oven (Cat.# G2545A, Agilent technologies, Santa Clara, CA, US), according to the manufacturer’s instructions. After 17 hours hybridization, slides were washed in staining dishes (Cat.# 121, Thermo Shandon, Waltham, MA, US) with Gene Expression Wash Buffer Kit(Cat.# 5188-5327, Agilent technologies, Santa Clara, CA, US)
Scan protocol Slides were scanned immediately after washing on the Agilent DNA Microarray Scanner (G2505B) using one color scan setting for 1x44k array slides (Scan Area 61x21.6 mm, Scan resolution 10um, Dye channel is set to Green and Green PMT is set to 100%).
Description gene expression in rBMSCs after cultured on Ta-modified surface
Data processing Slides were scanned by Agilent Microarray Scanner (Cat#G2565CA, Agilent technologies, Santa Clara, CA, US) with default settings, Dye channel: Green, Scan resolution=3μm, PMT 100%, 20bit. Data were extracted with Feature Extraction software 12.0 (Agilent technologies, Santa Clara, CA, US). Raw data were normalized by Quantile algorithm, limma packages in R.
 
Submission date Nov 17, 2020
Last update date Nov 18, 2020
Contact name junyu shi
E-mail(s) sakyamuni_jin@163.com
Organization name Shanghai Ninth People’s Hospital
Department Department of Implant Dentistry
Street address 639 zhi-zao-ju road
City Shanghai
ZIP/Postal code 200011
Country China
 
Platform ID GPL22145
Series (1)
GSE161611 circRNAs, miRNAs and mRNAs expression profiling in rBMSCs affected by Ta-modified Ti surface or simple Ti surface

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

Data table
ID_REF VALUE
1 8.575048e+003
2 2.810131e+000
3 2.816938e+000
4 2.823170e+000
5 6.178242e+000
6 2.945800e+000
7 2.837042e+000
8 3.760070e+002
9 4.469292e+001
10 2.845009e+000
11 2.846369e+000
12 4.006388e+004
13 5.068054e+002
14 3.224683e+001
15 1.044686e+002
16 4.171372e+000
17 5.140949e+001
18 2.615114e+003
19 2.838873e+000
20 2.835872e+000

Total number of rows: 62976

Table truncated, full table size 1219 Kbytes.




Supplementary file Size Download File type/resource
GSM4910781_Ta_3_257403610933_S001_GE1_1200.txt.gz 12.2 Mb (ftp)(http) TXT
Processed data included within Sample table
Processed data provided as supplementary file

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