|
| Status |
Public on Oct 24, 2011 |
| Title |
Medicago truncatula Nodule |
| Sample type |
SRA |
| |
|
| Source name |
Nodule
|
| Organism |
Medicago truncatula |
| Characteristics |
accession/ecotype: A17
tissue: Nodule
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Medicago small RNA libraries (except MTR01) were constructed and sequenced at Illumina; all other legume libraries plus MTR01 were constructed as previously described (Lu et al. 2007) and sequenced on an Illumina Genome Analyzer II instrument at the Delaware Biotechnology Institute. PARE library was constructed as previously described (German et al. 2008)
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
size fractionation |
| Instrument model |
Illumina Genome Analyzer II |
| |
|
| Description |
MND1
Processed data contain distinct smallRNAs with their raw abundance after removing the adapter sequences
|
| Data processing |
Adapter sequences were removed using a Perl script, generating small RNA sequences plus abundances . Twenty-one small RNA libraries were made the materials described above, representing four legume species, including eight libraries from M. truncatula, seven from Glycine max (soybean), two from Arachis hypogaea (peanut), and four from Phaseolus vulgaris (common bean); one PARE library was made from Medicago flower.These libraries were sequenced on an Illumina GAII, generating ~62 million small RNA sequences after removing adapters and low-quality reads, with trimmed lengths between 18 and 34 nucleotides. After excluding small RNAs matching structural RNAs (t/rRNA loci), 12.1 million and 12.6 million reads were mapped to the M. truncatula genome (Mt3.5) (http://www.medicago.org) and the Glycine max genome (Gmax101) (Schmutz et al., 2010), respectively.
|
| |
|
| Submission date |
Jul 29, 2011 |
| Last update date |
May 15, 2019 |
| 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 |
GPL11345 |
| Series (1) |
| GSE31061 |
miRNAs target conserved motifs of diverse genes encoding NB-LRRs to trigger trans-acting siRNAs in legumes. |
|
| Relations |
| SRA |
SRX087136 |
| BioSample |
SAMN00690755 |
