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Sample GSM1076153 Query DataSets for GSM1076153
Status Public on Feb 01, 2013
Title TGF beta1 treated for 48h #2
Sample type RNA
 
Channel 1
Source name human lung fibroblasts MRC-5 cells
Organism Homo sapiens
Characteristics cell line: lung fibroblasts MRC-5
agent: TGF beta1
time: 48h
Treatment protocol After overnight serum starvation, cells were treat with TGF beta1 for 48 h or 96 h
Growth protocol MEM containing 10% FBS, 37 degree and 5% CO2
Extracted molecule total RNA
Extraction protocol Total RNA extracted using Qiagen RNAeasy kit following manufacturer's instructions
Label Hy3
Label protocol 1000 ng total RNA from sample and reference was labelled with Hy3™ and Hy5™ fluorescent label, respectively, using the miRCURY™ LNA Array power labelling kit (Exiqon, Denmark) following the procedure described by the manufacturer
 
Channel 2
Source name common reference (pooled total RNA from human lung fibroblasts MRC-5 cells that were untreated, treated with TGF beta1 for 48 and 96h)
Organism Homo sapiens
Characteristics cell line: lung fibroblasts MRC-5
sample type: common reference (pooled total RNA of equal amount of the 9 samples)
Treatment protocol After overnight serum starvation, cells were treat with TGF beta1 for 48 h or 96 h
Growth protocol MEM containing 10% FBS, 37 degree and 5% CO2
Extracted molecule total RNA
Extraction protocol Total RNA extracted using Qiagen RNAeasy kit following manufacturer's instructions
Label Hy5
Label protocol 1000 ng total RNA from sample and reference was labelled with Hy3™ and Hy5™ fluorescent label, respectively, using the miRCURY™ LNA Array power labelling kit (Exiqon, Denmark) following the procedure described by the manufacturer
 
 
Hybridization protocol The Hy3™-labeled samples and a Hy5™-labeled reference RNA sample were mixed pair-wise and hybridized to the miRCURY™ LNA Array version 5th Generation (Exiqon, Denmark), which contains capture probes targeting all miRNAs for human, mouse or rat registered in the miRBASE version 15.0 at the Sanger Institute. The hybridization was performed according to the miRCURY™ LNA array manual using a Tecan HS4800 hybridization station (Tecan, Austria)
Scan protocol After hybridization the microarray slides were scanned and stored in an ozone free environment (ozone level below 2.0 ppb) in order to prevent potential bleaching of the fluorescent dyes. The miRCURY™ LNA array microarray slides were scanned using the Agilent G2565BA Microarray Scanner System (Agilent Technologies, Inc., USA) and the image analysis was carried out using the ImaGene 8.0 software (BioDiscovery, Inc., USA).
Description Biological replicate 2 of 3. MRC-5 cells, TGF beta1 treated for 48h.
'1_Exiqon*.txt' and '0_Exiqon*.txt' represent the raw data for Hy3 and Hy5, respectively.
Data processing The quantified signals were background corrected (Normexp with offset value 10 – Ritchie et al., 2007) and normalized using the global Lowess (LOcally WEighted Scatterplot Smoothing) regression algorithm.
 
Submission date Feb 01, 2013
Last update date Feb 01, 2013
Contact name Gang Liu
Organization name University of Alabama at Birmingham
Department Medicine
Street address 901 19TH ST S
City Birmingham
State/province Alabama
ZIP/Postal code 35294
Country USA
 
Platform ID GPL11432
Series (1)
GSE43992 miRNA in human lung fibroblasts

Data table header descriptions
ID_REF
VALUE normalized log2 ratio (Hy3/Hy5)

Data table
ID_REF VALUE
46572 0.391970386
46271 0.488038405
42613 0.496008103
42761 0.185754244
42511 0.808105397
46642 0.04584759
11217 0.545030084
42855 0.395767217
42770 0.069143845
11207 0.118671593
46558 0.396715507
42501 0.386987779
42756 0.045530966
11230 -0.138665726
14257 -0.466479322
42539 -0.154310692
17618 0.381318792
17295 0.201184164
28520 0.142985214
32825 0.178205055

Total number of rows: 2026

Table truncated, full table size 36 Kbytes.




Supplementary file Size Download File type/resource
GSM1076153_0_Exiqon_14180353_S01.txt.gz 794.8 Kb (ftp)(http) TXT
GSM1076153_1_Exiqon_14180353_S01.txt.gz 890.5 Kb (ftp)(http) TXT
Processed data included within Sample table

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