|
| Status |
Public on Mar 01, 2013 |
| Title |
mix3 rep2 |
| Sample type |
RNA |
| |
|
| Source name |
placenta
|
| Organism |
Homo sapiens |
| Characteristics |
spike-in hsa-mir-147: 10
spike-in hsa-mir-211: 0.1
spike-in hsa-mir-219-5p: 1
spike-in hsa-mir-338-3p: 10
spike-in hsa-mir-383: 0.1
spike-in hsa-mir-429: 1
precursor spike-in hsa-mir-147: 0
o-methyl spike-in hsa-mir-211: 0
o-methyl spike-in hsa-mir-219-5p: 0
precursor spike-in hsa-mir-338-3p: 0
precursor spike-in hsa-mir-383: 0
o-methyl spike-in hsa-mir-429: 0
|
| 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 |
biotin
|
| Label protocol |
500 ng RNA was labeled using Flashtag RNA labeling kit (Genisphere #HSR10FTA). Briefly, RNA underwent a PolyA tailing reaction using 2.5 mM MnCl2, ATP and PolyA Polymerase, followed by ligation of the biotinylated 3DNA signal molecule to the RNA sample
|
| |
|
| Hybridization protocol |
Samples were hybridized to a GeneChip miRNA 2.0 Array (Affymetrix) at 48°C and 60 rpm for 16 hours, then washed and stained on Fluidics Station 450 (Fluidics script FS450_0003)
|
| Scan protocol |
Chips were scanned on a GeneChip Scanner 3000 7G (Affymetrix)
|
| Description |
fmol of spiked oligos per 1mg of total RNA
|
| Data processing |
The data were analyzed with Affymetrix miRNA QC tool and normalized using default parameters, and batch corrected using Partek default, human probes were selected.
|
| |
|
| Submission date |
Sep 11, 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 |
GPL14613 |
| Series (2) |
| GSE40772 |
Differences in miRNA Detection Levels are Technology and Sequence Dependent [Affymetrix array] |
| GSE40820 |
Differences in miRNA Detection Levels are Technology and Sequence Dependent |
|
