|
| Status |
Public on Jun 01, 2011 |
| Title |
PH 36 hours replicate rat #1 |
| Sample type |
mixed |
| |
|
| Channel 1 |
| Source name |
rat liver
|
| Organism |
Rattus norvegicus |
| Characteristics |
strain: Sprague-Dawley
tissue: liver
procedure: Partial Hepatectomy
time: 36 hours
|
| Treatment protocol |
Partial Hepatectomies. Male Sprague-Dawley rats (Harlan Sprague-Dawley, Indianapolis, IN) ~ 175 g were subjected to sham surgery or 70% PH as originally described (18) between 8 AM and noon. At times between 3 and 72 hrs after surgery, the animals were sacrificed by exsanguinations under anesthesia; the liver remnants harvested and immediately frozen in liquid nitrogen. All animal work was approved by the Institutional Animal Care and Use Committee at the University of Minnesota and received humane care according to the criteria outlined in the Guide for the Care and Use of Laboratory Animals prepared by the National Academy of Sciences and published by the National Institutes of Health (NIH publication 86-23 revised 1985).
|
| Growth protocol |
Rats were purchased and maintained in central animal facilties at the University of Minnesota.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Trizol® reagent (Invitrogen) was used to extract total RNA from tissues
|
| Label |
DY547
|
| Label protocol |
Total RNA was ligated to a synthetic linker, 5’-pCU-DY547-3’. Reference DNA oligonucleotides (Invitrogen) complementary to a subset of mammalian miRNAs were combined and labeled with a ULYSIS® Alexa Fluor® 647 kit.
|
| |
|
| Channel 2 |
| Source name |
Reference DNA
|
| Organism |
Homo sapiens |
| Characteristics |
reference: synthetic DNA oligos corrresponding to human miRNAs
|
| Treatment protocol |
Partial Hepatectomies. Male Sprague-Dawley rats (Harlan Sprague-Dawley, Indianapolis, IN) ~ 175 g were subjected to sham surgery or 70% PH as originally described (18) between 8 AM and noon. At times between 3 and 72 hrs after surgery, the animals were sacrificed by exsanguinations under anesthesia; the liver remnants harvested and immediately frozen in liquid nitrogen. All animal work was approved by the Institutional Animal Care and Use Committee at the University of Minnesota and received humane care according to the criteria outlined in the Guide for the Care and Use of Laboratory Animals prepared by the National Academy of Sciences and published by the National Institutes of Health (NIH publication 86-23 revised 1985).
|
| Growth protocol |
Rats were purchased and maintained in central animal facilties at the University of Minnesota.
|
| Extracted molecule |
other |
| Extraction protocol |
Trizol® reagent (Invitrogen) was used to extract total RNA from tissues
|
| Label |
Alexa Fluor® 647
|
| Label protocol |
Total RNA was ligated to a synthetic linker, 5’-pCU-DY547-3’. Reference DNA oligonucleotides (Invitrogen) complementary to a subset of mammalian miRNAs were combined and labeled with a ULYSIS® Alexa Fluor® 647 kit.
|
| |
|
| |
| Hybridization protocol |
A mixture of labeled RNA and DNA was hybridized to a miRNA microarray (Thomson et al., 2005), inside a MAUI mixer in a MAUI hybridization system (BioMicro® System, Inc, Salt Lake City, UT, USA). Thomson, J.M., Parker, J., Perou, C.M., and S.M. Hammond. 2004. A custom microarray platform for analysis of microRNA gene expression. Nat. Methods 1: 47-53. Epub 2004 Sep 29.
|
| Scan protocol |
Slides were scanned with a ScanArray 5000 machine (Perkin Elmer®, Waltham, MA, USA).
|
| Data processing |
BlueFuse (BlueGenome, Cambridge, UK) was used to quantify pixel intensities. GeneSpring GX 7.3.1 (Agilent Technologies) was used for data normalization.
Data processed by Bluefuse is absolute value (attached to the Series record as a supplementary file), and from GeneSpring is U46 normalized ratio test/ref (in Sample data table below).
|
| |
|
| Submission date |
Apr 05, 2011 |
| Last update date |
Jun 01, 2011 |
| Contact name |
Yan Zeng |
| E-mail(s) |
zengyan@njau.edu.cn
|
| Organization name |
Nanjing Agricultural University
|
| Street address |
XuanWu District, No.1 WeiGang
|
| City |
Nanjing |
| State/province |
Jiangsu |
| ZIP/Postal code |
210095 |
| Country |
China |
| |
|
| Platform ID |
GPL9142 |
| Series (1) |
| GSE28404 |
Genome-wide MicroRNA Downregulation as a Negative Feedback Mechanism in the Early Phases of Liver Regeneration |
|
