|
| Status |
Public on Apr 03, 2020 |
| Title |
memory_gen1-1 |
| Sample type |
SRA |
| |
|
| Source name |
Arabidopsis thaliana Col-0
|
| Organism |
Arabidopsis thaliana |
| Characteristics |
replicate type: biological rep 1
tissue: rosette leaves
ecotype: Columbia-0
genotype/variation: memory line
|
| Treatment protocol |
Two memory plants, and four Col-0 wild-type plants were used. Leaves at bolting were flash freezed in liquid nitrogen. Tissues were ground by motor and pestle in liquid nitrogen.
|
| Growth protocol |
Seeds were sown on peat mix in square pots in reach-in chambers at 12hrs daylenght (22 °C, 120-150 μmol/(m^2*s) light)
|
| Extracted molecule |
total RNA |
| Extraction protocol |
sRNA extraction using NucleoSpin miRNA Plant Kit (Macherey-Nagel, Germany)
sRNA-seq libraries were constructed using the Illumina TruSeq Small RNA Sample Preparation Kit and sequenced on a BGISEQ-500 with a single-end 50-bp run length
|
| |
|
| Library strategy |
ncRNA-Seq |
| Library source |
transcriptomic |
| Library selection |
size fractionation |
| Instrument model |
BGISEQ-500 |
| |
|
| Data processing |
Trimmed data provided by BGI-Tech (Shenzhen, China) were used for the downstream processing
Small RNA-seq data were aligned to the Arabidopsis thaliana genome assembly (version TAIR10) using ShortStack (version 3.8.3; https://github.com/MikeAxtell/ShortStack/releases; Johnson et al., 2016) with default parameters except that the 'align-only' switch was activated
Each library was individually aligned, followed by merging the resultant bam files using samtools merge (Li et al., 2009)
Resulting clusters were used for control and treatment comparison
Genome_build: Arabidopsis thaliana genome assembly (version TAIR10)
Supplementary_files_format_and_content: tab-delimited file, <seqnames/chromosome> <start position> <end position> <strand> <name/cluster name> <counts>
|
| |
|
| Submission date |
Jul 09, 2019 |
| Last update date |
Apr 03, 2020 |
| Contact name |
Hardik Kundariya |
| E-mail(s) |
hsk13@psu.edu
|
| Organization name |
The Pennsylvania State University
|
| Street address |
361 N. Frear
|
| City |
University Park |
| State/province |
PA |
| ZIP/Postal code |
16801 |
| Country |
USA |
| |
|
| Platform ID |
GPL24025 |
| Series (1) |
| GSE134028 |
Small RNA sequencing of msh1 memory line and with isogenic Col-0 wild-type control in Arabidopsis |
|
| Relations |
| BioSample |
SAMN12236745 |
| SRA |
SRX6420514 |
