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Sample GSM5253217 Query DataSets for GSM5253217
Status Public on Apr 30, 2023
Title BGC-R
Sample type RNA
 
Source name BGC-R
Organism Homo sapiens
Characteristics cell type: BGC-R
Treatment protocol BGC-R and SGC-R cells were changed to no cisplatin medium for one week, and cells were havested together with BGC823 and SGC7901 under normal culture condition.
Growth protocol BGC823 and SGC7901 cells are maintained in RPMI1640 plus 10%FBS. BGC-R and SGC-R cells are maintained in RPMI1640 plus 10%FBS and 0.5μg/ml cisplatin
Extracted molecule total RNA
Extraction protocol RNA quantity and quality were measured by NanoDrop ND-1000. RNA integrity was assessed by standard denaturing agarose gel electrophoresis.
Label Cy3
Label protocol Sample labeling and array hybridization were performed according to the Agilent One-Color Microarray-Based Gene Expression Analysis protocol (Agilent Technology) with minor modifications. Briefly, mRNA was purified from total RNA after removal of rRNA (mRNA-ONLY™ Eukaryotic mRNA Isolation Kit, Epicentre). Then, each sample was amplified and transcribed into fluorescent cRNA along the entire length of the transcripts without 3' bias utilizing a random priming method (Arraystar Flash RNA Labeling Kit, Arraystar). The labeled cRNAs were purified by RNeasy Mini Kit (Qiagen). The concentration and specific activity of the labeled cRNAs (pmol Cy3/μg cRNA) were measured by NanoDrop ND-1000.
 
Hybridization protocol 1 μg of each labeled cRNA was fragmented by adding 5 μl 10 × Blocking Agent and 1 μl of 25 × Fragmentation Buffer, then heated the mixture at 60°C for 30 min, finally 25 μl 2 × GE Hybridization buffer was added to dilute the labeled cRNA. 50 μl of hybridization solution was dispensed into the gasket slide and assembled to the LncRNA expression microarray slide. The slides were incubated for 17 hours at 65°C in an Agilent Hybridization Oven. The hybridized arrays were washed, fixed and scanned with using the Agilent DNA Microarray Scanner (part number G2505C).
Scan protocol Slides were scanned immediately after washing on the Agilent DNA Microarray Scanner (G2505C) using one color scan setting for 8x60k array slides.
Description Gene expression of BGC-R
Data processing Agilent Feature Extraction software (version 11.0.1.1) was used to analyze acquired array images. Quantile normalization and subsequent data processing were performed with using the GeneSpring GX v12.1 software package (Agilent Technologies). After quantile normalization of the raw data, LncRNAs and mRNAs that at least 3 out of 4 samples have flags in Present or Marginal (“All Targets Value”) were chosen for further data analysis. Differentially expressed LncRNAs and mRNAs with statistical significance between the two groups were identified through P-value/FDR filtering. Differentially expressed LncRNAs and mRNAs between the two samples were identified through Fold Change filtering. Hierarchical Clustering and combined analysis were performed using homemade scripts.
 
Submission date Apr 19, 2021
Last update date Apr 30, 2023
Contact name Lifeng Feng
E-mail(s) lffeng@zju.edu.cn
Organization name Zhejiang University, School of Medicine, Sir Run Run Shaw Hospital
Street address No.3 East Qingchun Road
City Hangzhou
State/province Zhejiang
ZIP/Postal code 310016
Country China
 
Platform ID GPL16956
Series (1)
GSE172364 Development of gene expression signatures for cisplatin resistance in gastric cancer cells

Data table header descriptions
ID_REF
VALUE Normalized signal intensity

Data table
ID_REF VALUE
ASHGA5P058197 2.3582609
ASHGA5P007773 5.3641934
ASHGA5P031162 5.2483344
ASHGA5P041796 14.106913
ASHGA5P006930 7.2540083
ASHGA5P031496 6.9551506
ASHGA5P050699 11.861225
ASHGA5P035298 3.1948931
ASHGA5P014867 5.145999
ASHGA5P008172 3.245165
ASHGA5P047663 3.1839921
ASHGA5P012016 7.931669
ASHGA5P007747 8.428614
ASHGA5P026943 2.3582609
ASHGA5P035562 4.839177
ASHGA5P018786 9.78393
ASHGA5P001180 4.729143
ASHGA5P023786 5.8279195
ASHGA5P021269 2.3582609
ASHGA5P000239 2.70399

Total number of rows: 58944

Table truncated, full table size 1360 Kbytes.




Supplementary file Size Download File type/resource
GSM5253217_2.txt.gz 2.6 Mb (ftp)(http) TXT
Processed data included within Sample table

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