NCBI Logo
GEO Logo
   NCBI > GEO > Accession DisplayHelp Not logged in | LoginHelp
GEO help: Mouse over screen elements for information.
          Go
Sample GSM1034382 Query DataSets for GSM1034382
Status Public on May 03, 2013
Title Control2 vs. Treatment1 at 3hr [mRNA]
Sample type RNA
 
Channel 1
Source name Control mouse 2
Organism Mus musculus
Characteristics gender: female
strain: C57BL/6
group: Control
agent: none
time point: 3hr
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 cy3
Label protocol Total RNAs from liver were isolated with a miRNeasy column (Qiagen, Valencia, CA), and both Cy3 and Cy5-labeled samples were prepared with two color labeling kits (Agilent Technologies, Santa Clara, CA), then hybridized at 65°C for 17 h.
 
Channel 2
Source name Treatment mouse 1
Organism Mus musculus
Characteristics gender: female
strain: C57BL/6
group: Treatment
agent: 350mg/kg of acetaminophen
time point: 3hr
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 cy5
Label protocol Total RNAs from liver were isolated with a miRNeasy column (Qiagen, Valencia, CA), and both Cy3 and Cy5-labeled samples were prepared with two color labeling kits (Agilent Technologies, Santa Clara, CA), then hybridized at 65°C for 17 h.
 
 
Hybridization protocol Labeled samples were hybridized to Agilent Whole Mouse Genome Microarray as described in 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 3hr
Data processing Scanned data was processed using Agilent Feature Extraction
 
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 GPL10333
Series (2)
GSE42178 Affect of liver transcriptome by acute acetaminophen exposure [mRNA]
GSE42182 Affect of liver transcriptome by acute acetaminophen exposure

Data table header descriptions
ID_REF
VALUE log2(rProcessedSignal/gProcessedSignal) from Feature Extraction output

Data table
ID_REF VALUE
1 0.39188926
2 0
3 0
4 0
5 0
6 0
7 0
8 0
9 0
10 0
11 0
12 -0.22167367
13 0
14 -0.22296813
15 0.009841458
16 -0.098220262
17 0.076003735
18 0
19 0
20 -0.7580204

Total number of rows: 44397

Table truncated, full table size 644 Kbytes.




Supplementary file Size Download File type/resource
GSM1034382_20110517_bl6_apap_c2_3hr_v_bl6_apap_t1_3hr.txt.gz 15.1 Mb (ftp)(http) TXT
Processed data included within Sample table

| NLM | NIH | GEO Help | Disclaimer | Accessibility |
NCBI Home NCBI Search NCBI SiteMap