|
| Status |
Public on Oct 01, 2008 |
| Title |
Small RNA SBS signatures: mutant mop1-1 |
| Sample type |
MPSS |
| |
|
| Source name |
mutant mop1-1
|
| Organism |
Zea mays |
| Characteristics |
Maize variety K55
Immature ears harvested 68 days after germination
Maize mop1-1 (MEDIATOR OF PARAMUTATION1) mutant. Ortholog of the Arabidopsis RDR2 gene.
|
| Biomaterial provider |
University of Arizona. Vicki Chandler's group.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Trizol
|
| |
|
| Description |
This library was derived from maize variety K55. Immature ears were harvested from plants grown outdoors in Tuscon, AZ. The material was harvested from plants 68 days after germination, with the floral tissue including young tassels 2-3 cm long. Total RNA was isolated using a standard TRIZOL-based method and the small RNA libraries were generated as described by Lu et al. (Methods 2007, 43:110), followed by sequencing with Illumina's SBS method. The adapter sequences were removed, and the abundance of each distinct small RNA was determined.
|
| Data processing |
Small RNA molecules were sequenced using Illumina's SBS technology (Genome Analyzer 1). Potential 3' adapter sequence was trimmed off from the signatures and only the signautres longer than equal to 15 nt were kept for analysis. Since the maize genomic sequence and annotation have not yet been completed, we were not able identify the complete set of genome-matching small RNAs nor those that match to regulatory RNAs. We normalized the expression level of all small RNAs in the set to 5 million (TP5M), which is close the number of total small RNA signautres sequenced. Note that we used Illumina's first generation Genome Analyzer and the pipeline for SBS sequencing.
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| |
|
| Submission date |
Jul 19, 2008 |
| Last update date |
Sep 27, 2008 |
| Contact name |
Blake C. Meyers |
| E-mail(s) |
bmeyers@danforthcenter.org
|
| Phone |
314-587-1422
|
| Organization name |
Donald Danforth Plant Science Center
|
| Lab |
Meyers lab
|
| Street address |
975 N Warson Road
|
| City |
St. Louis |
| State/province |
MO |
| ZIP/Postal code |
63132 |
| Country |
USA |
| |
|
| Platform ID |
GPL7071 |
| Series (1) |
| GSE12173 |
Small RNA SBS signatures identified from maize using Illumina's SBS technology |
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