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Sample GSM865737 Query DataSets for GSM865737
Status Public on Mar 25, 2012
Title BLCL_1.2
Sample type RNA
 
Source name EBV-transformed lymphoblastoid cell line from subject 1.2
Organism Homo sapiens
Characteristics cell type: EBV-transformed lymphoblastoid cells
origin: lymphoid
subject: 1.2
Treatment protocol Not treated.
Growth protocol B-LCLs and B cells were grown in RPMI 1640 medium supplemented with 25mM HEPES, 2mM L-glutamine, 10% heat-inactivated fetal bovine serum and penicillin-streptomycin. HEK293 and HeLa cells were grown in DMEM medium supplemented with 2mM L-glutamine, 10% heat-inactivated fetal bovine serum and penicillin-streptomycin. Exponential growth under normal conditions.
Extracted molecule total RNA
Extraction protocol Total RNA was isolated with the miRNeasy mini kit, including on-column DNase I treatment (Qiagen), according to the manufacturer’s instructions. Total RNA was quantified using the NanoDrop 2000 (Thermo Scientific) and RNA quality was assessed with the 2100 Bioanalyzer (Agilent Technologies).
Label Cy3
Label protocol 100 ng of each RNA sample was labeled with the microRNA complete labeling and hybridization kit (Agilent Technologies) according to the manufacturer’s instructions.
 
Hybridization protocol Labeled RNA was hybridized to the Agilent Human microRNA Microarray Release 16.0 (G4872A-031181 Agilent Technologies) with the microRNA complete labeling and hybridization kit (Agilent Technologies) according to the manufacturer’s instructions.
Scan protocol Slides were scanned with a GenePix 4000B scanner (Molecular Devices) at a 5uM/pixel resolution .
Data processing Features were extracted with the GenePix 6.1 software. Analyses were performed using BRB-ArrayTools Version 4.2.0 Stable Release developed by Dr. Richard Simon and the BRB-ArrayTools Development Team (http://en.bio-soft.net/chip/BRBArrayTools.html). The data were background-subtracted and quantile normalized. To estimate a single intensity measure for each miRNA, we calculated the mean of its different probes.
 
Submission date Jan 24, 2012
Last update date Mar 25, 2012
Contact name Diana Paola Granados
Organization name IRIC
Department Medecine
Lab Immunobiologie
Street address C.P. 6128, succursale Centre-ville
City Montreal
State/province Quebec
ZIP/Postal code H3C 3J7
Country Canada
 
Platform ID GPL15159
Series (1)
GSE35319 MHC I-associated peptides preferentially derive from transcripts bearing miRNA response elements

Data table header descriptions
ID_REF
VALUE Log2 normalized signal intensity

Data table
ID_REF VALUE
A_25_P00010019 10.70824718
A_25_P00010020 10.24083805
A_25_P00010021 9.585082054
A_25_P00010023 9.660155296
A_25_P00010041 9.821048737
A_25_P00010042 9.612874985
A_25_P00010043 9.559628487
A_25_P00010044 9.480194092
A_25_P00010047 10.56726742
A_25_P00010048 10.02403736
A_25_P00010053 13.67903996
A_25_P00010054 13.01393604
A_25_P00010062 9.626076698
A_25_P00010063 9.458078384
A_25_P00010070 11.27604961
A_25_P00010071 10.16347313
A_25_P00010072 10.15421295
A_25_P00010073 9.779792786
A_25_P00010078 13.77147293
A_25_P00010079 13.06768703

Total number of rows: 3523

Table truncated, full table size 92 Kbytes.




Supplementary file Size Download File type/resource
GSM865737.txt.gz 3.0 Mb (ftp)(http) TXT
Processed data included within Sample table

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