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Sample GSM901210 Query DataSets for GSM901210
Status Public on Dec 26, 2020
Title non-rejection_plasma_replicate 4
Sample type RNA
 
Source name non-rejection plasma
Organism Rattus norvegicus
Characteristics tissue: plasma
gender: male
Treatment protocol Freshly drawn blood was collected on the 7thday after OLT in ethylenediaminetetraacetic acid (EDTA)-treated tubes. Within 30 minutes, the tubes were centrifuged at 820g for 10 min. Then, 1-ml aliquots of plasma were transferred to 1.5-ml tubes and centrifuged at 16,000g for 10 min to pellet any remaining cellular debris. Liver grafts of each animal were obtained and conserved in liquid nitrogen until use.
Growth protocol Inbred male Lewis and BN rats weighing 200-250g were maintained in laminar flow cages in a specific pathogen-free animal facility with a standard diet and water.
Extracted molecule total RNA
Extraction protocol Total RNA was extracted from plasma samples with the mirVana PARIS miRNA Isolation Kit (Ambion, Austin, TX) and from tissue samples with the mirVana miRNA Isolation Kit (Ambion). RNA concentrations were determined with a NanoDrop 1000 Spectrophotometer (NanoDrop Technologies, Waltham, MA)
Label Cy3
Label protocol RNA was labeled with Cy3 according to the protocols of the Agilent microRNA microarray system
 
Hybridization protocol Each slide was hybridized with 100 ng Cy3-labeled RNA with the miRNA Complete Labeling and Hyb Kit (Agilent Technologies, Santa Clara, CA) in a hybridization oven (Agilent Technologies) at 55°C and 20 rpm for 20 hours according to the manufacturer’s instructions.
Scan protocol Microarray slides were scanned by an XDR Scan (PMT100, PMT5) according to the protocols of the Agilent microRNA microarray system
Description XM40plasma
Data processing The microarray image data were converted into spot intensity values with Feature Extraction Software Rev. 9.5.3 (Agilent Technologies). The signal minus background values were exported directly into GeneSpring GX10 software (Agilent Technologies), and the raw data were normalized by the Quantile algorithm.
 
Submission date Mar 26, 2012
Last update date Dec 26, 2020
Contact name jie hu
Organization name Zhongshan hospital, Fudan University
Street address 180 Fenglin Road
City Shanghai
ZIP/Postal code 200032
Country China
 
Platform ID GPL10906
Series (1)
GSE36798 Development of microRNA signatures for acute rejection after liver transplantation using rat model

Data table header descriptions
ID_REF
VALUE Normalized signal intensity

Data table
ID_REF VALUE
rno-let-7a 5.7545133
rno-let-7b 5.7034864
rno-let-7b* 3.6071188
rno-let-7c 5.455915
rno-let-7d 5.2121396
rno-let-7d* 4.76468
rno-let-7e 0.8187354
rno-let-7e* 0.031407066
rno-let-7f 5.822906
rno-let-7i 5.5337143
rno-let-7i* 0.031662192
rno-miR-1 2.1509373
rno-miR-1* 0.2758738
rno-miR-100 0.68054175
rno-miR-101a 4.9860206
rno-miR-101a* 0.031842556
rno-miR-101b 7.8310986
rno-miR-103 2.808233
rno-miR-106b 5.7881904
rno-miR-106b* 0.031439655

Total number of rows: 350

Table truncated, full table size 7 Kbytes.




Supplementary file Size Download File type/resource
GSM901210_XM40plasma.txt.gz 430.5 Kb (ftp)(http) TXT
Processed data included within Sample table

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