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Sample GSM901209 Query DataSets for GSM901209
Status Public on Dec 26, 2020
Title non-rejection_plasma_replicate 3
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 XM38plasma
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 6.572978
rno-let-7b 5.92464
rno-let-7b* 6.037479
rno-let-7c 5.6465263
rno-let-7d 5.0363708
rno-let-7d* 5.7034864
rno-let-7e 1.3136543
rno-let-7e* 0.032019723
rno-let-7f 6.6381903
rno-let-7i 6.703227
rno-let-7i* 0.031674687
rno-miR-1 3.6378129
rno-miR-1* 4.8023257
rno-miR-100 1.2761315
rno-miR-101a 1.2888049
rno-miR-101a* 0.032492325
rno-miR-101b 3.557361
rno-miR-103 2.8993628
rno-miR-106b 4.895681
rno-miR-106b* 0.03146648

Total number of rows: 350

Table truncated, full table size 7 Kbytes.




Supplementary file Size Download File type/resource
GSM901209_XM38plasma.txt.gz 419.0 Kb (ftp)(http) TXT
Processed data included within Sample table

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