|
| Status |
Public on Sep 01, 2015 |
| Title |
Seedling_degradome1_raw |
| Sample type |
SRA |
| |
|
| Source name |
Degradome
|
| Organism |
Phaseolus vulgaris |
| Characteristics |
ecotype: Negro Jamapa
tissue: seedling
|
| Growth protocol |
moist vermiculite watered to substrate capacity and maintained at 24°C for 48 hours with 16h/8h light/dark day cycles
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA was isolated from frozen samples using the Trizol reagent according to manufacturer's instructions (Invitrogen, Carlsbad, CA) and 40 µg of each sample were prepared
The protocol used to obtain cDNA libraries for degradome analysis was carried out essentially as previously described (Addo-Quaye et al, 2008; German et al, 2009)
|
| |
|
| Library strategy |
OTHER |
| Library source |
transcriptomic |
| Library selection |
other |
| Instrument model |
Illumina Genome Analyzer IIx |
| |
|
| Description |
Degradome
|
| Data processing |
Library strategy: degradome-Seq
raw reads from the Illumina Pipeline 1.4 for the small RNA libraries were cleaned of sequence adapters, low quality tags and small sequences (< 16 nt long)
Genome_build: Phaseolus vulgaris v1.0 (Common bean)
Supplementary_files_format_and_content: sequences and counts
|
| |
|
| Submission date |
Mar 30, 2015 |
| Last update date |
May 15, 2019 |
| Contact name |
Damien Formey |
| E-mail(s) |
damien.formey@gmail.com
|
| Organization name |
UNAM
|
| Department |
Center for Genomic Science
|
| Lab |
Functional Genomics Eukaryotes Research Program
|
| Street address |
Avenida de la Universidad
|
| City |
Cuernavaca |
| State/province |
Morelos |
| ZIP/Postal code |
62210 |
| Country |
Mexico |
| |
|
| Platform ID |
GPL19961 |
| Series (2) |
| GSE67432 |
Genome-wide identification of the Phaseolus vulgaris sRNAome using small RNA and degradome sequencing [degradome-seq] |
| GSE67433 |
Genome-wide identification of the Phaseolus vulgaris sRNAome using small RNA and degradome sequencing |
|
| Relations |
| BioSample |
SAMN03451462 |
| SRA |
SRX973380 |
