 |
 |
GEO help: Mouse over screen elements for information. |
|
| Status |
Public on Dec 01, 2014 |
| Title |
Dassel leaves (flagellin treated 30 minutes), rep 1 |
| Sample type |
SRA |
| |
|
| Source name |
soybean leaves
|
| Organism |
Glycine max |
| Characteristics |
tissue: soybean leaves
cultivar: Dassel
treatment: flagellin treated 30 minutes
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Small RNA libraries were constructed from total RNA isolated from soybean using Plant RNA Reagent (Invitrogen, Life Technologies, USA). The sRNA library preparation protocol is based on Illumina’s sRNA Sequencing Sample Preparation Guide (Illumina, San Diego, CA). The libraries were sequenced on an Illumina HiSeq 2000 at the Delaware Biotechnology Institute (Newark, DE). Degradome libraries (PARE) constructed from total RNA isolated from soybean using Plant RNA Reagent (Invitrogen, Life Technologies, USA). The libraries were constructed as previously described (Zhai et al. 2009 PMID: 23810899). The libraries were sequenced on an Illumina HiSeq 2000 at the Delaware Biotechnology Institute (Newark, DE).
|
| |
|
| Library strategy |
miRNA-Seq |
| Library source |
transcriptomic |
| Library selection |
size fractionation |
| Instrument model |
Illumina HiSeq 2000 |
| |
|
| Data processing |
Small RNA-seq: the adapter sequences were trimmed from raw sequence reads, and then the small RNA sequences were trimmed to the lengths between 15 and 34 nucleotides. Small RNA reads were mapped to the soybean genome.
PARE-seq: the adapter sequences were trimmed from raw sequence reads, and then the PARE sequences were trimmed to the lengths between 18 and 21 nucleotides. PARE reads were mapped to the soybean genome.
Genome_build: The Soybean (Glycine max) genome; JGI Glyma1
Supplementary_files_format_and_content: Text containing distinct smallRNAs with their raw abundance after removing the adapter sequences
|
| |
|
| Submission date |
Jun 24, 2014 |
| Last update date |
May 15, 2019 |
| Contact name |
Blake C. Meyers |
| E-mail(s) |
[email protected]
|
| 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 |
GPL15008 |
| Series (1) |
| GSE58779 |
Characterization of small RNAs and their targets in soybean (Glycine max) |
|
| Relations |
| BioSample |
SAMN02870822 |
| SRA |
SRX621780 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSM1419354_DasFlag_1_chopped.txt.gz |
21.5 Mb |
(ftp)(http) |
TXT |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data provided as supplementary file |
|
|
|
|
 |
