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Sample GSM2420149 Query DataSets for GSM2420149
Status Public on Dec 31, 2016
Title MDA_48H_tdt8
Sample type RNA
 
Source name MDA MB-231, 48H, NLC-Blank, replicate 2
Organism Homo sapiens
Characteristics cell line: MDA MB-231
cell type: Breast cancer cells
Treatment protocol NLC-Citral, Citral and NLC-Blank were diluted in the fresh media before treated the cells for 48 hours. The cells were incubated in the incubator for 48 hours post treatment.
Growth protocol MDA MB-231 cells was purchased from ATCC and sub-cultured under under certain conditioned (37°C+5% CO2) in cell culture media with 10% fetal bovine serum.
Extracted molecule total RNA
Extraction protocol Total RNA of the cells was extracted by using RNAeasy mini prep kit (Qiagen, USA) by following the manufacturer's recommendations.
Label Cy3
Label protocol Cyanine-3 (Cy3) labeled cRNA was prepared from 0.5 ug RNA using the One-Color Low RNA Input Linear Amplification PLUS 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 1.5 ug of Cy3-labelled cRNA (specific activity >10.0 pmol Cy3/ug cRNA) was fragmented at 60°C for 30 minutes in a reaction volume of 250 ml containing 1x Agilent fragmentation buffer and 2x Agilent blocking agent following the manufacturers instructions. On completion of the fragmentation reaction, 250 ml of 2x Agilent hybridization buffer was added to the fragmentation mixture and hybridized to Agilent Whole Human Genome Oligo Microarrays (G4112A) 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 dried immediately by brief centrifugation.
Scan protocol Slides were scanned immediately after washing on the Agilent DNA Microarray Scanner using one color scan setting for 2x60k array slides
Description Gene expression of control
Data processing The scan images were analyzed with the feature extraction sofware 13.1 using default parameters by the Agilent Inc.
 
Submission date Dec 08, 2016
Last update date Dec 31, 2016
Contact name Noraini Nordin
E-mail(s) noraini90.nordin@gmail.com
Phone 6012-2922337
Organization name University Putra Malaysia
Department Cell Biology
Lab ANIMAL TISSUE CULTURE
Street address Animal Tissue Culture Lab
City Serdang
State/province selangor
ZIP/Postal code 43400
Country Malaysia
 
Platform ID GPL13607
Series (1)
GSE91047 Regulated gene expression for breast cancer cells treated with NLC-Citral for 48 hours

Data table header descriptions
ID_REF
VALUE Normalized signal intensity

Data table
ID_REF VALUE
4 1.44E+02
5 2.76E+00
6 2.77E+00
7 3.91E+02
8 1.61E+03
9 2.79E+00
10 2.79E+00
11 3.11E+00
12 1.01E+02
13 5.31E+01
14 4.64E+02
15 3.27E+01
16 2.81E+00
17 7.04E+01
18 2.81E+00
19 2.81E+00
20 2.81E+00
21 2.80E+00
22 5.87E+00
23 2.80E+00

Total number of rows: 62973

Table truncated, full table size 911 Kbytes.




Supplementary file Size Download File type/resource
GSM2420149_SG14124392_252800421714_S001_GE1_1200_Jun14_2_4_SAM_8.txt.gz 3.0 Mb (ftp)(http) TXT
Processed data included within Sample table

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