|
| Status |
Public on Aug 16, 2013 |
| Title |
col0 |
| Sample type |
SRA |
| |
|
| Source name |
unopened flower buds
|
| Organism |
Arabidopsis thaliana |
| Characteristics |
genotype: wild-type
ecotype: Col-0
|
| Growth protocol |
Plants were grown on soil in 16 hours of light and 8 hours of dark
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Briefly, smRNA-seq libraries were produced using the Small RNA Sample Prep v1.5 kit (Illumina, San Diego, CA) as per manufacturerâs instruction.
|
| |
|
| Library strategy |
ncRNA-Seq |
| Library source |
transcriptomic |
| Library selection |
size fractionation |
| Instrument model |
Illumina Genome Analyzer II |
| |
|
| Description |
smRNA from wild-type Col-0 plants
|
| Data processing |
Raw smRNA-seq reads were first trimmed for 3'-adapters using the VectorStrip program that is part of the EBI EMBOSS package. At least 8 nt of the adapter sequences were required for successful trimming; the remaining untrimmed reads were discarded. Successfully trimmed reads were reduced to non-redundant sequences (NR-seq) and mapped to Arabidopsis genome (TAIR9 assembly) as described previously (Zheng et al., 2010), with maximum 8% mismatches allowed. All the clone-abundance and alignment information were loaded into local MySQL databases for further queries.
|
| |
|
| Submission date |
Apr 11, 2011 |
| Last update date |
May 23, 2014 |
| Contact name |
Qi Zheng |
| E-mail(s) |
qi.zheng@nemours.org
|
| Phone |
3026515778
|
| Organization name |
Nemours Children's Health
|
| Street address |
1701 Rockland Road
|
| City |
Wilmington |
| State/province |
DE |
| ZIP/Postal code |
19803 |
| Country |
USA |
| |
|
| Platform ID |
GPL9302 |
| Series (2) |
| GSE28512 |
DCP5, a highly conserved P-body-nucleating protein, regulates multiple small RNA-mediated silencing pathways in Arabidopsis (smRNA-seq) |
| GSE28524 |
DCP5, a highly conserved P-body-nucleating protein, regulates multiple small RNA-mediated silencing pathways in Arabidopsis |
|
| Relations |
| BioSample |
SAMN02052590 |
