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Sample GSM1034507 Query DataSets for GSM1034507
Status Public on May 03, 2013
Title Control2 vs. Treatment1 at 24hr [miRNA]
Sample type RNA
 
Channel 1
Source name Control mouse 2
Organism Mus musculus
Characteristics strain: C57BL/6
gender: female
group: Control
agent: none
time point: 24hr
Treatment protocol To study the global changes of transcriptome in the liver after acetaminophen overdose. Eight week old female C57BL/6 mice were fasted for 24 hours prior to a single intraperitoneal injection of 350mg/kg of acetaminophen in phosphate buffer saline (PBS) (treatment group) or PBS (control group). The mice were euthanized at different time points post exposure; plasma and tissue samples were collected for pathological examination and biochemical analyses.
Extracted molecule total RNA
Extraction protocol Liver samples were collected from different time points after mice had been exposed to acetaminophen. Total RNA from liver was extracted with the miRNeasy kit (Qiagen, Germantown, MD), as described. The quality and quantity of the RNA were evaluated with Agilent 2100 Bioanalyzer (Santa Clara, CA) and NanoDrop 1000 spectrophotometer
Label Hy3
Label protocol Total RNAs from liver were labeled with Hy3 and Hy5 dye with labeling kits from Exiqon then hybridized at 56°C for 16 h.
 
Channel 2
Source name Treatment mouse 1
Organism Mus musculus
Characteristics strain: C57BL/6
gender: female
group: Treatment
agent: 350mg/kg of acetaminophen
time point: 24hr
Treatment protocol To study the global changes of transcriptome in the liver after acetaminophen overdose. Eight week old female C57BL/6 mice were fasted for 24 hours prior to a single intraperitoneal injection of 350mg/kg of acetaminophen in phosphate buffer saline (PBS) (treatment group) or PBS (control group). The mice were euthanized at different time points post exposure; plasma and tissue samples were collected for pathological examination and biochemical analyses.
Extracted molecule total RNA
Extraction protocol Liver samples were collected from different time points after mice had been exposed to acetaminophen. Total RNA from liver was extracted with the miRNeasy kit (Qiagen, Germantown, MD), as described. The quality and quantity of the RNA were evaluated with Agilent 2100 Bioanalyzer (Santa Clara, CA) and NanoDrop 1000 spectrophotometer
Label Hy5
Label protocol Total RNAs from liver were labeled with Hy3 and Hy5 dye with labeling kits from Exiqon then hybridized at 56°C for 16 h.
 
 
Hybridization protocol Labeled samples were hybridized to Exiqon 5th generation miRCURY LNA microRNA array according to the manufacturer's protocol.
Scan protocol After hybridization, the slides were washed and scanned with a scanner from Agilent (Santa Clara, CA).
Description Control2 vs. Treatment1 at 24hr
Data processing Scanned data was processed using AnalyzerDG software. Cy3 and Cy5 (high energy scanned) intensities were normalized using LOWESS
 
Submission date Nov 09, 2012
Last update date May 03, 2013
Contact name Ji-Hoon Cho
E-mail(s) jcho@systemsbiology.org
Organization name Institute for Systems Biology
Street address 401 Terry Avenue North
City Seattle
State/province WA
ZIP/Postal code 98109
Country USA
 
Platform ID GPL14957
Series (2)
GSE42181 Affect of liver transcriptome by acute acetaminophen exposure [miRNA]
GSE42182 Affect of liver transcriptome by acute acetaminophen exposure

Data table header descriptions
ID_REF
VALUE Log2 (Hy5/Hy3), normalized by LOWESS

Data table
ID_REF VALUE
2 -0.437185567
3 -0.64291408
4 -1.276872814
5 -0.32844709
6 -1.27792621
7 -0.478800233
8 -1.283075903
9 -0.49431208
10 -0.345076809
11 -0.98161705
12 -1.180830869
13 -1.566663167
14 -0.887279835
16 -0.283985434
17 -0.046535133
18 0.033105408
19 -0.465792186
20 0.148808114
21 -0.674023932
22 -0.504872868

Total number of rows: 9120

Table truncated, full table size 154 Kbytes.




Supplementary file Size Download File type/resource
GSM1034507_20110512_BL6_APAP_C2_24h_v_BL6_APAP_T1_24h.csv.gz 908.1 Kb (ftp)(http) CSV
Processed data included within Sample table

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