|
Status |
Public on Feb 25, 2010 |
Title |
P19(Lin28)-day4b |
Sample type |
RNA |
|
|
Channel 1 |
Source name |
transfected P19 EC cells
|
Organism |
Mus musculus |
Characteristics |
cell line: mouse P19 cells, stably transfected with plasmid constitutively expressing human LIN28
|
Treatment protocol |
P19 and P19+Lin28A cells differentiated to 5 days with Retinoic acid/aggregation to induce neurogenesis by standard methods.
|
Growth protocol |
P19 cells were grown in maintained in alpha-MEM supplemented with 2.5% fetal bovine serum, 7.5% bovine serum, and 50 units/mL of penicillin/streptomycin. P19_Lin28 cells were maintained in the same medium with 2 microg/mL puromycin .
|
Extracted molecule |
total RNA |
Extraction protocol |
Total RNA was purified using the miRNA isolation kit (Ambion, Austin, TX, USA).
|
Label |
Hy3
|
Label protocol |
One µg total RNA from sample and reference was labeled with Hy3™ and Hy5™ fluorescent label, respectively, using the miRCURY™ LNA Array power labeling kit (Exiqon, Denmark) following the procedure described by the manufacturer.
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|
|
Channel 2 |
Source name |
common reference pool
|
Organism |
Mus musculus |
Characteristics |
cell line: mouse P19 cells
|
Extracted molecule |
total RNA |
Extraction protocol |
Total RNA was purified using the miRNA isolation kit (Ambion, Austin, TX, USA).
|
Label |
Hy5
|
Label protocol |
One µg total RNA from sample and reference was labeled with Hy3™ and Hy5™ fluorescent label, respectively, using the miRCURY™ LNA Array power labeling kit (Exiqon, Denmark) following the procedure described by the manufacturer.
|
|
|
|
Hybridization protocol |
The Hy3™-labeled samples and a Hy5™-labeled reference RNA sample were mixed pair-wise and hybridized to the miRCURY™ LNA array version 11.0 (Exiqon, Denmark), which contains capture probes targeting all miRNAs for human, mouse or rat registered in the miRBASE version 13.0 at the Sanger Institute. The hybridization was performed according to the miRCURY™ LNA array manual using a Tecan HS4800 hybridization station (Tecan, Austria).
|
Scan protocol |
The miRCURY™ LNA array microarray slides were scanned using the Agilent G2565BA Microarray Scanner System (Agilent Technologies, Inc., USA) and the image analysis was carried out using the ImaGene 7.0 software (BioDiscovery, Inc., USA)
|
Description |
biological replicate 2 of 2
|
Data processing |
The quantified signals were background corrected (Normexp with offset value 10 – Ritchie et al., 2007) and normalized using the global Lowess (LOcally WEighted Scatterplot Smoothing) regression algorithm.
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|
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Submission date |
Jan 12, 2010 |
Last update date |
Feb 25, 2010 |
Contact name |
Eric Moss |
E-mail(s) |
mosseg@umdnj.edu
|
Phone |
8565662896
|
Fax |
8565662691
|
Organization name |
UMDNJ
|
Department |
Molecular Biology
|
Street address |
2 Medical Center Dr.
|
City |
Stratford |
State/province |
NJ |
ZIP/Postal code |
08084 |
Country |
USA |
|
|
Platform ID |
GPL7722 |
Series (1) |
GSE19858 |
Effect of LIN28 on miRNA profile at day 5 of neurogliogenesis in vitro |
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