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Sample GSM4150526 Query DataSets for GSM4150526
Status Public on Nov 30, 2020
Title liver_MMI_rep1
Sample type RNA
 
Channel 1
Source name liver_MMI_rep1
Organism Mus musculus
Characteristics tissue: liver
Treatment protocol Mice were rendered hypothyroid by the addition of 0.1% methimazole (MMI) and 1% NaClO4 in their drinking water for two weeks . To identify hepatic miRNAs that have maximal T3 responsiveness, hypothyroid mice were injected intraperitoneally with a single dose of T3 (5μg/20g body weight).
Growth protocol Mice were rendered hypothyroid by the addition of 0.1% methimazole (MMI) and 1% NaClO4 in their drinking water for two weeks . To identify hepatic miRNAs that have maximal T3 responsiveness, hypothyroid mice were injected intraperitoneally with a single dose of T3 (5μg/20g body weight).
Extracted molecule total RNA
Extraction protocol RNA was prepared using TRIZOL following the manufacturer's recommendations. RNA was quantified using a NanoDrop-1000 spectrophotometer and quality was monitored with the Agilent 2100 Bioanalyzer (Agilent Technologies, Santa Clara, CA).
Label Hy5
Label protocol Cyanine-3 (Cy3) labeled cRNA was prepared from 0.5 ug RNA using the One-Color Low RNA Input Linear Amplification PLUS kit (Agilent) according to the manufacturer's instructions, followed by RNAeasy column purification (QIAGEN, Valencia, CA). Dye incorporation and cRNA yield were checked with the NanoDrop ND-1000 Spectrophotometer.
 
Channel 2
Source name liver_MMI+T3_rep1
Organism Mus musculus
Characteristics tissue: liver
Treatment protocol Mice were rendered hypothyroid by the addition of 0.1% methimazole (MMI) and 1% NaClO4 in their drinking water for two weeks . To identify hepatic miRNAs that have maximal T3 responsiveness, hypothyroid mice were injected intraperitoneally with a single dose of T3 (5μg/20g body weight).
Growth protocol Mice were rendered hypothyroid by the addition of 0.1% methimazole (MMI) and 1% NaClO4 in their drinking water for two weeks . To identify hepatic miRNAs that have maximal T3 responsiveness, hypothyroid mice were injected intraperitoneally with a single dose of T3 (5μg/20g body weight).
Extracted molecule total RNA
Extraction protocol RNA was prepared using TRIZOL following the manufacturer's recommendations. RNA was quantified using a NanoDrop-1000 spectrophotometer and quality was monitored with the Agilent 2100 Bioanalyzer (Agilent Technologies, Santa Clara, CA).
Label Hy3
Label protocol Cyanine-3 (Cy3) labeled cRNA was prepared from 0.5 ug RNA using the One-Color Low RNA Input Linear Amplification PLUS kit (Agilent) according to the manufacturer's instructions, followed by RNAeasy column purification (QIAGEN, Valencia, CA). Dye incorporation and cRNA yield were checked with the NanoDrop ND-1000 Spectrophotometer.
 
 
Hybridization protocol 1.5 ug of Cy3-labelled cRNA (specific activity >10.0 pmol Cy3/ug cRNA) was fragmented at 60°C for 30 minutes in a reaction volume of 250 ml containing 1x Agilent fragmentation buffer and 2x Agilent blocking agent following the manufacturers instructions. On completion of the fragmentation reaction, 250 ml of 2x Agilent hybridization buffer was added to the fragmentation mixture and hybridized to Agilent Whole Human Genome Oligo Microarrays (G4112A) for 17 hours at 65°C in a rotating Agilent hybridization oven. After hybridization, microarrays were washed 1 minute at room temperature with GE Wash Buffer 1 (Agilent) and 1 minute with 37°C GE Wash buffer 2 (Agilent), then dried immediately by brief centrifugation.
Scan protocol Slides were scanned immediately after washing on the Agilent DNA Microarray Scanner (G2505B) using one color scan setting for 1x44k array slides (Scan Area 61x21.6 mm, Scan resolution 10um, Dye channel is set to Green and Green PMT is set to 100%).
Data processing The scanned images were analyzed with Feature Extraction Software 9.1 (Agilent) using default parameters (protocol GE1-v1_91 and Grid: 012391_D_20060331) to obtain background subtracted and spatially detrended Processed Signal intensities. Features flagged in Feature Extraction as Feature Non-uniform outliers were excluded.
log(MMI+T3/MMI)
 
Submission date Nov 05, 2019
Last update date Dec 01, 2020
Contact name Dandan Zhang
E-mail(s) zhangdandan3@hotmail.com
Organization name Fudan University
Street address Dongan Road
City Shanghai
ZIP/Postal code 230000
Country China
 
Platform ID GPL20794
Series (1)
GSE139961 Differentially expressed microRNAs in the mouse liver with T3 treatment

Supplementary file Size Download File type/resource
GSM4150526_Raw_Intensity_File.xls.gz 123.7 Kb (ftp)(http) XLS
GSM4150526_processed_data.txt.gz 4.9 Kb (ftp)(http) TXT
Processed data provided as supplementary file

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