|
| Status |
Public on Mar 01, 2013 |
| Title |
mix4 rep2 |
| Sample type |
RNA |
| |
|
| Source name |
placenta
|
| Organism |
Homo sapiens |
| Characteristics |
type of replicate: biological replicate 2
spike-in hsa-mir-147: 0
spike-in hsa-mir-211: 0
spike-in hsa-mir-219-5p: 0
spike-in hsa-mir-338-3p: 0
spike-in hsa-mir-383: 0
spike-in hsa-mir-429: 0
precursor spike-in hsa-mir-147: 0.1
o-methyl spike-in hsa-mir-211: 1
o-methyl spike-in hsa-mir-219-5p: 10
precursor spike-in hsa-mir-338-3p: 0.1
precursor spike-in hsa-mir-383: 1
o-methyl spike-in hsa-mir-429: 10
|
| Treatment protocol |
Oligos representing mature, modified and precursor miRNA were artificially introduced to native RNA
|
| Growth protocol |
RNA Purchased (see extract protocol).
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Commercial human placenta RNA was purchased from Ambion (AM7950) in two lots: 03070032 and 1004005.
|
| Label |
Cy3
|
| Label protocol |
100 ng RNA was labeled using miRNA complete labeling and hyb kit (Agilent #5190-0456) with Cy3-pCp following diphosphorylation. Desalting done using micro-bio spin columns.
|
| |
|
| Hybridization protocol |
Labeled RNA was hybridized with a 8X15 Human miRNA array rel 14 v2 (design number 29297) at 55°C and 20 rpm for 20 hours, and then washed according to the manufacturer’s instructions.
|
| Scan protocol |
Scanning was performed on an Agilent Scanner using 5uM resolution.
|
| Description |
fmol of spiked oligos per 1mg of total RNA
|
| Data processing |
gProcessedSignals processed without batch correction.
The signal intensity was set to the maximum of either "TotalGeneSignal" or the "TotalGeneError" in the GeneView file. Batch correction was performed using the Partek software defaults. The signal intensities were log2 transformed and scaled by quantile normalization.
|
| |
|
| Submission date |
Sep 12, 2012 |
| Last update date |
Mar 01, 2013 |
| Contact name |
Dena Leshkowitz |
| E-mail(s) |
dena.leshkowitz@weizmann.ac.il
|
| Organization name |
Weizmann Institute of Science
|
| Department |
Bioinformatics Unit, Life Sciences Core Facilities
|
| Street address |
P.O.B. 26
|
| City |
Rehovot |
| ZIP/Postal code |
76100 |
| Country |
Israel |
| |
|
| Platform ID |
GPL14943 |
| Series (2) |
| GSE40815 |
Differences in miRNA Detection Levels are Technology and Sequence Dependent [Agilent array] |
| GSE40820 |
Differences in miRNA Detection Levels are Technology and Sequence Dependent |
|
