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Sample GSM1480706 Query DataSets for GSM1480706
Status Public on Jan 01, 2015
Title HeLa_heat-shock_vs_control_rep1
Sample type RNA
 
Channel 1
Source name heat-shock_treated_rep1
Organism Homo sapiens
Characteristics cell line: HeLa cell
treatment: heat-shock treated RNA
Treatment protocol Heat shock stress was induced by subjecting the cells to the temperature of 45°C for 30 minutes, in water bath. Cells were subsequently transferred to the incubator for two hours. Before subjecting to heat shock, cells were washed with 1X PBS twice and then fresh media was added for proper quantization of heat shock response.
Growth protocol HeLa cell line was used which was procured from National Center for Cell Science, Pune, India. Cells were maintained in Dulbecco’s modified Eagle’s medium (DMEM) supplemented with heat inactivated 10% fetal bovine serum (FBS) from GIBCO and 1% antibiotic antimycotic solution from HiMedia, at 37°C in 5% CO2 and 95% atmosphere incubator.
Extracted molecule total RNA
Extraction protocol Total RNA used for the whole-genome expression profiling of miRNA was isolated using Trizol (Invitrogen), according to the manufacturer’s instructions. Further, RNA was purified using RNeasy purification kit from Qiagen to remove residual aromatic compounds that may hinder with microarray expression.
Label Cy5
Label protocol 1µg of total RNA was used for 5'-dephosphorylation of miRNAs using calf intestinal phosphatase (CIP). Spike-in miRNAs were also added for experimental control. Subsequently, samples were fluorescently labeled with Hy3 or Hy5 to the 3'-end of the miRNAs. The complementary samples labeled with Hy3 or Hy5 were combined on ice and added onto the slide placed in the slide chamber for hybridization.
 
Channel 2
Source name heat-shock_control_rep1
Organism Homo sapiens
Characteristics cell line: HeLa
treatment: control RNA
Treatment protocol Heat shock stress was induced by subjecting the cells to the temperature of 45°C for 30 minutes, in water bath. Cells were subsequently transferred to the incubator for two hours. Before subjecting to heat shock, cells were washed with 1X PBS twice and then fresh media was added for proper quantization of heat shock response.
Growth protocol HeLa cell line was used which was procured from National Center for Cell Science, Pune, India. Cells were maintained in Dulbecco’s modified Eagle’s medium (DMEM) supplemented with heat inactivated 10% fetal bovine serum (FBS) from GIBCO and 1% antibiotic antimycotic solution from HiMedia, at 37°C in 5% CO2 and 95% atmosphere incubator.
Extracted molecule total RNA
Extraction protocol Total RNA used for the whole-genome expression profiling of miRNA was isolated using Trizol (Invitrogen), according to the manufacturer’s instructions. Further, RNA was purified using RNeasy purification kit from Qiagen to remove residual aromatic compounds that may hinder with microarray expression.
Label Cy3
Label protocol 1µg of total RNA was used for 5'-dephosphorylation of miRNAs using calf intestinal phosphatase (CIP). Spike-in miRNAs were also added for experimental control. Subsequently, samples were fluorescently labeled with Hy3 or Hy5 to the 3'-end of the miRNAs. The complementary samples labeled with Hy3 or Hy5 were combined on ice and added onto the slide placed in the slide chamber for hybridization.
 
 
Hybridization protocol Samples were incubated for 16-18 hrs. in a water bath. Post-incubation, slides were washed rigorously and scanned.
Scan protocol After drying, chips were scanned using Perkin Elmer scanner at 10µM resolution and PMT of 60.
Description Replicate 1
Data processing The .gpr files were obtained from Perkin Elmer scanner. The arrays were dye-swapped and gene-specific dye-bias correction was applied using the GASSCO method (Margaritis et al., Mol. Sys. Biol. 5:266 (2009)) implemented in the “dyebias” BioConductor package. For normalization, Lowess method is used. The uploaded processed data files contain Lowess normalized log2 test/control ratios.
 
Submission date Aug 18, 2014
Last update date Jan 01, 2015
Contact name Mitali Mukerji
E-mail(s) mitali@igib.res.in
Phone 91-11-29879302
Organization name CSIR-Institute Of Genomics and Integrative Biology
Department Functional Genomics and Molecular Medicine
Lab 319
Street address Sukhdev Vihar, Mathura Road
City New Delhi
State/province New Delhi
ZIP/Postal code 110020
Country India
 
Platform ID GPL9908
Series (1)
GSE60472 Whole genome miRNA expression profiling using HeLa cells in response to Heat shock stress.

Data table header descriptions
ID_REF
VALUE Lowess normalized log2 ratio of test/control

Data table
ID_REF VALUE
1
2 0.077497841
3 -9.306238011
4 2.751828329
5
6
7 -0.776544832
8 1.029015429
9
10
11
12 -1.19682125
13 0.795177323
14
15
16
17
18
19 -0.158387223
20

Total number of rows: 9360

Table truncated, full table size 95 Kbytes.




Supplementary file Size Download File type/resource
GSM1480706_HeLa_heat-shock_vs_control_rep1.gpr.gz 864.8 Kb (ftp)(http) GPR
Processed data included within Sample table

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