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Sample GSM865739 Query DataSets for GSM865739
Status Public on Mar 25, 2012
Title BLCL_2.2
Sample type RNA
 
Source name EBV-transformed lymphoblastoid cell line from subject 2.2
Organism Homo sapiens
Characteristics cell type: EBV-transformed lymphoblastoid cells
origin: lymphoid
subject: 2.2
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 10.2382431
A_25_P00010020 10.06262875
A_25_P00010021 9.543718338
A_25_P00010023 9.675012589
A_25_P00010041 9.558057785
A_25_P00010042 9.466889381
A_25_P00010043 9.461671829
A_25_P00010044 9.679811478
A_25_P00010047 11.18356991
A_25_P00010048 10.82377148
A_25_P00010053 13.50503063
A_25_P00010054 12.69622803
A_25_P00010062 9.816514969
A_25_P00010063 9.569312096
A_25_P00010070 11.21985435
A_25_P00010071 11.10986519
A_25_P00010072 11.17311478
A_25_P00010073 10.4601469
A_25_P00010078 13.64530277
A_25_P00010079 12.70088387

Total number of rows: 3523

Table truncated, full table size 92 Kbytes.




Supplementary file Size Download File type/resource
GSM865739.txt.gz 2.8 Mb (ftp)(http) TXT
Processed data included within Sample table

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