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Sample GSM1151678 Query DataSets for GSM1151678
Status Public on Feb 13, 2014
Title MCF7_Hypoxia_32h_rep3 [miRNA]
Sample type RNA
 
Source name MCF7_Hypoxia_32h
Organism Homo sapiens
Characteristics oxygen: 1%
time: 32h
Treatment protocol Exposure of cell cultures to hypoxia (1% oxygen) was undertaken in an In vivo2 Hypoxia Work Station (Ruskin Technologies) in parallel with cells maintained in normoxic conditions (21% oxygen). Cells were recovered after 16h, 32h and 48h of exposure to hypoxia.
Growth protocol MCF-7 cells were grown in Dulbecco's Modified Eagle Medium supplemented with 10% fetal bovine serum and 2mmol/L of L-glutamine
Extracted molecule total RNA
Extraction protocol RNA was extracted from cells using the miRVana miRNA isolation kit (Ambion) in accordance with the prescribed protocol provided with the kit. RNA quality was assessed after extraction using Agilent bioanalyser.
Label Cy3
Label protocol 100µg of total RNA were first dephosphorylated using Calf Instestine Alkaline Phosphatase (New England Biolabs). Single molecules of Cyanine 3-pCp provided in the miRNA Labeling Reagent and Hybridization kit (Agilent) were ligated to the 3' end of the dephosphorylated RNA molecules using T4 RNA ligase (New England Biolabs). Labeled RNAs were purified throughout micro Bio-Spin 6 columns (BioRad) and dried down using a speed-vacuum concentrator Savant ISS110 (Thermo Scientific). Samples were resuspended in 18µl of RNAse free water and prepared for hybridization by adding 4.5µl of 10X GE Blocking agent and 22.5µl of 2X Hi-RPM Hybridization Buffer (both in Agilent miRNA Labeling Reagent and hybridization kit).
 
Hybridization protocol The hybridization was performed at 55˚C for 20h and at a constant speed rotation of 20rpm.
Scan protocol After washing the microarrays with the Agilent Gene Expression Wash Buffer kit, the hybridization signals were detected by the Agilent Microarray scanner (G2565BA)and using the following settings: scan area 61 x 21.6 mm, scan resolution 5µm, 5µm scanning mode Single Pass, eXtended Dynamic range selected, Dye chanel set to green, green PMT set to XDR Hi 100% and XDR Lo 5%.
Description Total RNA containing short RNA fraction
Hypoxia_32h_R3
Data processing The scanned images were analyzed with Feature Extraction Software version 9.5.1 (Agilent). A GeneView file was generated for each of the samples and used for further analysis. The Total Gene signal from GeneView files was normalised using the vsn package from Bioconductor
 
Submission date May 30, 2013
Last update date Feb 13, 2014
Contact name Carme Camps
Organization name Wellcome Trust Centre for Human Genetics/ U. of Oxford
Street address Roosevelt Drive
City Oxford
ZIP/Postal code OX37BN
Country United Kingdom
 
Platform ID GPL8227
Series (2)
GSE47532 Integrated analysis of microRNA and mRNA expression and association with HIF binding in MCF-7 cells under hypoxia [miRNA]
GSE47534 Integrated analysis of microRNA and mRNA expression and association with HIF binding in MCF-7 cells under hypoxia

Data table header descriptions
ID_REF
VALUE Normalised signal intensity (vsn normalisation) from GeneView files

Data table
ID_REF VALUE
DarkCorner 2.288177538
NC1_00000197 3.511015384
NC1_00000215 4.212675741
NC2_00079215 3.013813894
NC2_00092197 3.269828204
NC2_00106057 3.910381361
NC2_00122731 3.235247941
NegativeControl 4.635231374
SCorner3 2.267149832
dmr_285 2.044161295
dmr_3 2.226697811
dmr_308 2.385709403
dmr_316 2.505331267
dmr_31a 2.180507524
dmr_6 2.596585325
ebv-miR-BART1-3p 2.102889196
ebv-miR-BART1-5p 2.061220381
ebv-miR-BART10 2.212337899
ebv-miR-BART10* 2.232147465
ebv-miR-BART11-3p 2.087531613

Total number of rows: 821

Table truncated, full table size 20 Kbytes.




Supplementary file Size Download File type/resource
GSM1151678_Hyp32hR3_FE.txt.gz 1.8 Mb (ftp)(http) TXT
GSM1151678_Hyp32hR3_GeneView.txt.gz 9.1 Kb (ftp)(http) TXT
Processed data included within Sample table

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