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Sample GSM1260453 Query DataSets for GSM1260453
Status Public on Oct 21, 2014
Title liver, syngeneic day5 rep.1
Sample type RNA
 
Source name liver, syngeneic day5
Organism Mus musculus
Characteristics strain: B10.BR (H2-Kk) mouse as donor and B10.D2 (H2-Kd) mouse for recipient
tissue: liver
gender: male
Treatment protocol B10.BR mice were used as donors and B10.D2 mice were used as recipients. Liver allo-transplantation surgery on the mice was performed in this combination. Three mice from each group were sacrificed, and the liver grafts were removed on days 5, 8, 14 and 100 after transplantation.
Growth protocol All mice were maintained under standard conditions and fed rodent food and water, in accordance with the guidelines of the Animal Use and Care Committee of the National Research Institute for Child Health and Development.
Extracted molecule total RNA
Extraction protocol Total RNA, including miRNA from RNAlater (Ambion, Austin, TX) immersed liver grafts, was isolated using the RNeasy Mini Kit and miRNeasy kit (QIAGEN Inc., Valencia, CA.), according to the manufacturer’s protocol. The quality and quantity of the RNA were evaluated using the NanoDrop 1000 (Thermo Scientific Inc., Waltham, MA) and Agilent 2100 Bioanalyzer (Agilent Technologies, Santa Clara, CA).
Label Cy3
Label protocol One hundred ng of total RNA was dephosphorylated with calf intestinal alkaline phosphatase (Takara Bio Inc., Shiga, Japan), followed by denaturing with heat in the presence of dimethyl sulfoxide (SIGMA-Aldrich Co., St. Louis, MO). A cyanine dye, cyanine3-cytidine bisphosphate (Agilent), was then joined to the dephosphorylated single-stranded RNA using T4RNA ligase (Ambion). MicroBioSpin 6 columns (Bio-Rad Laboratories Inc., Hercules, CA) were used to remove any unincorporated cyanine dye from the samples.
 
Hybridization protocol The purified labeled miRNA probes were hybridized to 8x15 K mouse miRNA microarrays (Agilent Technologies) in a rotating hybridization oven at 20 rpm for 20 hours at 55 °C. After hybridization, the arrays were washed in Gene Expression Wash Buffer 1 with Triton X-102 followed by Gene Expression Wash Buffer 2 with Triton X-102.
Scan protocol All slides were immediately scanned at a resolution of 5 µm with Green-PMT XDR Hi 100%, Lo 5% using an Agilent DNA Microarray Scan (Agilent). The resulting images were quantified using Agilent’s Feature Extraction software program. The differentially expressed miRNAs were identified using a standard protocol developed for miRNA gene arrays. To increase the reliability of the data and ease of detection, miRNA species with a hybridization intensity <1.5 times the average hybridization intensity (mean) were excluded from the analysis.
Description Gene expression after 5day in syngrafting liver
Data processing A miRNA clustering analysis was performed with the Hierarchical clustering algorithm provided in the Avadis, ArrayAssist 4.3 software package.
 
Submission date Nov 07, 2013
Last update date Oct 21, 2014
Contact name Masayuki Fujino
E-mail(s) mfujino-kkr@umin.ac.jp
Organization name NIID
Street address Toyama, Shinjuku-ku, 1-23-1
City Tokyo
ZIP/Postal code 162-8640
Country Japan
 
Platform ID GPL8824
Series (1)
GSE52164 Identification of microRNAs involved in acute rejection and spontaneous tolerance in murine hepatic allografts

Data table header descriptions
ID_REF
VALUE The data were normalized by quantile normalization using the Avadis 4.3 software (Strand Genomics).

Data table
ID_REF VALUE
DarkCorner -8.396265
NC1_00000197 -8.396265
NC1_00000215 -8.396265
NC2_00079215 -8.396265
NC2_00092197 -8.396265
NC2_00106057 -8.396265
NC2_00122731 -8.396265
NegativeControl -8.396265
SCorner3 -8.396265
dmr_285 -8.396265
dmr_3 -8.396265
dmr_308 -8.396265
dmr_316 -8.396265
dmr_31a -8.396265
dmr_6 -8.396265
hur_1 6.0545955
hur_2 9.376991
hur_4 6.368503
hur_5 -8.396265
hur_6 6.8232875

Total number of rows: 598

Table truncated, full table size 13 Kbytes.




Supplementary file Size Download File type/resource
GSM1260453_No_20.txt.gz 633.5 Kb (ftp)(http) TXT
Processed data included within Sample table

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