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Sample GSM2728859 Query DataSets for GSM2728859
Status Public on Aug 02, 2020
Title mice 3,1-3 (miRNA)
Sample type RNA
Source name control group
Organism Mus musculus
Characteristics strain: C57BL/6
Sex: male
age: 6 weeks
tissue: liver
agent: saline
dose: control
Treatment protocol Twenty-four C57BL/6 male mice were randomly divided into 3 groups: (1) vehicle control (n=8), (2) 270 mg/kg MCT (n=8), (3) 330 mg/kg MCT (n=8). Mice were fasted for 12 h before orally given with different doses of MCT (270, 330mg/kg, intragastric administration), but allowed water ad libitum. Mice were allowed food and water ad libitum after MCT administration. Animals were sacrificed 48 h after MCT administration, and blood and livers were collected.
Growth protocol Mice were supplied with standard laboratory diet and water ad libitum at a temperature 22±1 °C with a 12 h light–dark cycle (6:00–18:00) and 65±5% humidity. All mice were received humane care in compliance with the institutional animal care guidelines approved by the Experimental Animal Ethical Committee, Shanghai University of Traditional Chinese Medicine.
Extracted molecule total RNA
Extraction protocol Total RNA was isolated using TRIzol (Invitrogen) and miRNeasy mini kit (QIAGEN) according to manufacturer’s instructions, which efficiently recovered all RNA species, including miRNAs. RNA quality and quantity was measured by using nanodrop spectrophotometer (ND-1000, Nanodrop Technologies) and RNA Integrity was determined by gel electrophoresis
Label Hy3
Label protocol After RNA isolation from the samples, the miRCURY™ Hy3™/Hy5™ Power labeling kit (Exiqon, Vedbaek, Denmark) was used according to the manufacturer’s guideline for miRNA labelling. One microgram of each sample was 3'-end-labeled with Hy3TM fluorescent label, using T4 RNA ligase by the following procedure: RNA in 2.0 μL of water was combined with 1.0 μL of CIP buffer and CIP (Exiqon). The mixture was incubated for 30 min at 37°C, and was terminated by incubation for 5 min at 95°C. Then 3.0 μL of labeling buffer, 1.5 μL of fluorescent label (Hy3TM), 2.0 μL of DMSO, 2.0 μL of labeling enzyme were added into the mixture. The labeling reaction was incubated for 1 h at 16°C, and terminated by incubation for 15 min at 65°C.
Hybridization protocol After stopping the labeling procedure, the Hy3TM-labeled samples were hybridized on the miRCURYTM LNA Array (v.18.0) (Exiqon) according to array manual. The total 25 μL mixture from Hy3TM-labeled samples with 25 μL hybridization buffer were first denatured for 2 min at 95°C, incubated on ice for 2 min and then hybridized to the microarray for 16–20 h at 56°C in a 12-Bay Hybridization Systems (Hybridization System - Nimblegen Systems, Inc., Madison, WI, USA), which provides an active mixing action and constant incubation temperature to improve hybridization uniformity and enhance signal. Following hybridization, the slides were achieved, washed several times using Wash buffer kit (Exiqon), and finally dried by centrifugation for 5 min at 400 rpm. Then the slides were scanned using the Axon GenePix 4000B microarray scanner (Axon Instruments, Foster City, CA).
Scan protocol Slides were scanned using the Axon GenePix 4000B microarray scanner (Axon Instruments, Foster City, CA).Scanned images were then imported into GenePix Pro 6.0 software (Axon) for grid alignment and data extraction.
Description 1-3
Data processing Replicated miRNAs were averaged and miRNAs that intensities>=30 in all samples were chosen for calculating Median normalization factor. Expressed data were normalized using the Median normalization. After normalization, significant differentially expressed miRNAs were identified through Volcano Plot filtering. Hierarchical clustering was performed using MEV software (v4.6, TIGR)
Submission date Aug 02, 2017
Last update date Aug 02, 2020
Contact name Zhenlin Huang
Organization name Shanghai University of Traditional Chinese Medicine
Department Institute of Chinese Materia Medica
Lab Shanghai Key Laboratory of Complex Prescription
Street address 1200 Cailun Road, Zhangjiang High Tech Park
City Shanghai
State/province Shanghai
ZIP/Postal code 201203
Country China
Platform ID GPL23853
Series (1)
GSE102150 Integrative analysis of hepatic microRNA and mRNA to identify potential biological pathways associated with monocrotaline-induced liver injury in mice

Data table header descriptions
VALUE Normalized signal intensity

Data table
42638 0.094890511
42888 6.656934307
17278 0.052919708
42826 1.02189781
17537 0.312043796
46636 1.708029197
46276 0.003649635
46457 0.010948905
42469 0.00729927
27575 0.589416058
46481 0.018248175
46807 1.341240876
42821 0.156934307
46279 0.009124088
11052 1.468978102
42810 0.052919708
17506 6.260948905
42919 0.02189781
42937 0.009124088
28480 0.038321168

Total number of rows: 1178

Table truncated, full table size 19 Kbytes.

Supplementary file Size Download File type/resource
GSM2728859_1-3.gpr.gz 1010.6 Kb (ftp)(http) GPR
Processed data included within Sample table
Processed data are available on Series record

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