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Sample GSM1627733 Query DataSets for GSM1627733
Status Public on Mar 10, 2015
Title Dunn_86_2
Sample type RNA
 
Source name Osteosarcoma commercial human cell lines
Organism Mus musculus
Characteristics cell line: Dunn
properties: Osteoblastic
replicates: Passage number 86
Treatment protocol Dunn, LM8 cells were cultured in in Dulbecco’s Modified Eagle Medium (DMEM containing 4.5 g/l glucose)/Ham F12 (Invitrogen, Carlsbad, CA, USA) (1:1) supplemented with 10% fetal calf serum (FCS), 1 unit/ml penicillin G, and 1 μg/ml streptomycin. The cultures were incubated at 37 ºC in a humidified incubator with 5% CO2
Growth protocol Dunn, LM8 cells were cultured at same conditions and at 75% confulence the RNAs were isolated
Extracted molecule total RNA
Extraction protocol Total RNA was isolated using Rneasy MiniKit from Qiagen ( Valencia, CA, USA) following manufacturers instruction. RNA was quantified using a NanoDrop-1000 spectrophotometer and quality was monitored with the Agilent 2100 Bioanalyzer (Agilent Technologies, Santa Clara, CA).
Label Cy3
Label protocol Cyanine-3 (Cy3) labeled cRNA was prepared from 100 ng total RNA using the low input quick amplification labeling kit (Agilent) according to the manufacturer's instructions, followed by RNAeasy column purification (QIAGEN, Valencia, CA). Dye incorporation and cRNA yield were checked with the NanoDrop ND-1000 Spectrophotometer.
 
Hybridization protocol Mouse GE 4x44K v2 Microarrays were incubated for 17 hours at 65°C in a rotating Agilent hybridization oven. After hybridization, microarrays were washed 1 minute at room temperature with GE Wash Buffer 1 (Agilent) and 1 minute with 37°C GE Wash buffer 2 (Agilent), then immediately air dried prior scanning.
Scan protocol Slides were scanned immediately after washing on the Agilent DNA Microarray C reader using using a scan Control software version A.8.4.1 and one color scan setting for 4x44k array slides (Scan Area 61x21.6 mm, Scan resolution 5 um, Dye channel is set to Green and Green PMT is set to 100%).
Description Mouse osteosarcoma cell line
Data processing The scanned images were analyzed with Feature Extraction Software 10.7.3 (Agilent) using default parameters to obtain background subtracted and spatially detrended Processed Signal intensities.
 
Submission date Mar 09, 2015
Last update date Mar 10, 2015
Contact name Ram Mohan Ram Kumar
E-mail(s) rkumar@research.balgrist.ch
Organization name University Hospital Balgrist, University of Zurich, Zurich, Switzerland
Department Orthopaedics
Street address Forchstrasse 340
City Zurich
ZIP/Postal code 8008
Country Switzerland
 
Platform ID GPL10333
Series (2)
GSE66674 Identification of genes regulated during passaging of mouse osteosarcoma cell lines
GSE66675 Identification of genes regulated during passaging of human and mouse osteosarcoma cell lines

Data table header descriptions
ID_REF
VALUE Normalized intensity

Data table
ID_REF VALUE
1 4.81E+03
2 4.54E+00
3 4.46E+00
4 4.39E+00
5 4.33E+00
6 4.27E+00
7 4.22E+00
8 4.16E+00
9 4.12E+00
10 4.07E+00
11 4.04E+00
12 8.34E+00
13 1.44E+01
14 3.94E+00
15 7.67E+00
16 3.98E+03
17 1.06E+04
18 3.86E+00
19 4.16E+00
20 9.40E+01

Total number of rows: 44397

Table truncated, full table size 639 Kbytes.




Supplementary file Size Download File type/resource
GSM1627733_252665512133_SLOT01_S01_GE1_107_Sep09_1_2_Dunn_86_2.txt.gz 2.2 Mb (ftp)(http) TXT
Processed data included within Sample table
Processed data are available on Series record

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