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Sample GSM829377 Query DataSets for GSM829377
Status Public on Nov 10, 2011
Title B104 siRBM3 rep2
Sample type RNA
 
Source name B104 clonal cell line, transfected, 48 hours
Organism Mus musculus
Characteristics cell type: neuroblastoma
cell line: B104
knockdown: RBM3
Treatment protocol Cell lines were transfected with an siRNA duplex against RBM3 at a ratio of 20 nM siRNA per 25 ┬Ál Lipofectamine RNAiMax (Life Technologies) to knockdown RBM3, or mock treated as a control; cells were harvested after 48 hrs.
Growth protocol B104 cells were cultured in DMEM supplemented with 10% FBS, 200 mM L-glutamine and penicillin/streptomycin.
Extracted molecule total RNA
Extraction protocol The mirVana miRNA isolation kit (Life Technologies) was used to isolate miRNAs according to the manufactor's reccomendations. RNA was quantified using a NanoDrop-1000 spectrophotometer and quality was monitored with the Agilent 2100 Bioanalyzer (Agilent Technologies, Santa Clara, CA).
Label Cy3
Label protocol Cyanine-3 (Cy3) labeled cRNA was prepared from total RNA using the microRNA Spike-In Kit (Agilent) according to the manufacturer's instructions, followed by RNAeasy column purification (QIAGEN, Valencia, CA). Dye incorporation and cRNA yield were checked with the NanoDrop ND-1000 Spectrophotometer.
 
Hybridization protocol Hybridization was done according to Agilent's specifications.
Scan protocol Slides were scanned immediately after washing on the Agilent DNA Microarray Scanner (G2505B) using one color scan setting for 1x44k array slides (Scan Area 61x21.6 mm, Scan resolution 10um, Dye channel is set to Green and Green PMT is set to 100%).
Description microRNA expression 48 hours after RBM3 knockdown by siRNA transfection
Data processing Microarrays were analyzed with Genespring software. The Agilent Feature Extraction tool was used to obtain the signal values and detection above background for the Agilent chip. Processing of the data was performed within the Bioconductor project and the R program software (R is available as Free Software under the terms of the Free Software Foundation's GNU General Public License). The scale normalization method used was proposed by Yang et al [49, 50] and is further elaborated by Smyth and Speed [51]. Log-values were scaled to have the same median-absolute-deviation (MAD) across arrays. The 578 Human miRNAs were filtered down to 216 by excluding those miRNAs with signals not detected above background for all the samples.
 
Submission date Nov 07, 2011
Last update date Nov 10, 2011
Contact name Julie Pilotte
E-mail(s) pilotte.julie@gmail.com
Organization name The Scripps Research Institute
Department Neurobiology
Lab Peter Vanderklish
Street address 10550 North Torrey Pines Rd, Sbr-14
City La Jolla
State/province CA
ZIP/Postal code 92037
Country USA
 
Platform ID GPL8824
Series (1)
GSE33519 Microarray profiling reveals broad and differential effects of RBM3 on miRNA expression.

Data table header descriptions
ID_REF
VALUE Normalized signal intensity

Data table
ID_REF VALUE
mghv-miR-M1-2 62.0726
mmu-let-7a 908.777
mmu-let-7b 818.048
mmu-let-7c 890.512
mmu-let-7d 407.8
mmu-let-7e 156.819
mmu-let-7f 856.308
mmu-let-7g 261.198
mmu-let-7i 555.161
mmu-miR-1 676.895
mmu-miR-100 46.9432
mmu-miR-101b 42.3482
mmu-miR-103 151.149
mmu-miR-106a 97.8025
mmu-miR-106b 230.012
mmu-miR-107 124.438
mmu-miR-10a 71.8849
mmu-miR-10b 43.2718
mmu-miR-1224 6353.45
mmu-miR-125a-3p 157.304

Total number of rows: 577

Table truncated, full table size 12 Kbytes.




Supplementary file Size Download File type/resource
GSM829377_G4472A_004.txt.gz 646.2 Kb (ftp)(http) TXT
Raw data provided as supplementary file
Processed data included within Sample table

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