|
| Status |
Public on Nov 01, 2016 |
| Title |
nrpd1_rep1_sRNA-Seq |
| Sample type |
SRA |
| |
|
| Source name |
nrpd1_sRNA-Seq
|
| Organism |
Arabidopsis thaliana |
| Characteristics |
genotype/variation: nrpd1 mutant
age: 14 days
tissue: seedlings
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNAs were isolated from 14-d-old seedlings by Trizol reagent (Invitrogen).
Small RNAs were precipitated by PEG 8000 solution (20% PEG, 1 M NaCl). Small RNAs were sent to Genomics Core Facility of Shanghai Center for Plant Stress Biology for library preparation and Illumina sequencing.
|
| |
|
| Library strategy |
ncRNA-Seq |
| Library source |
transcriptomic |
| Library selection |
size fractionation |
| Instrument model |
Illumina HiSeq 2500 |
| |
|
| Data processing |
Briefly, after adapter sequences were trimmed, clean reads of size 18-31 nt were mapped to the Arabidopsis genome (TAIR10) using Bowtie (Langmead et al. 2009) with parameter -v 0 -k 10. Reads that can mapped to annotated structural RNAs were removed.
Genome_build: TAIR10
Supplementary_files_format_and_content: The bedGraph files were generated using genomeCoverageBed from bedtools with parameter -bga -split
|
| |
|
| Submission date |
Jun 28, 2016 |
| Last update date |
May 15, 2019 |
| Contact name |
Jian-Kang Zhu |
| E-mail(s) |
zhu132@purdue.edu
|
| Organization name |
Purdue University
|
| Department |
Department of Horticulture and Landscape Architecture
|
| Street address |
625 Agriculture Mall Dr.
|
| City |
West Lafayette |
| State/province |
IN |
| ZIP/Postal code |
47907 |
| Country |
USA |
| |
|
| Platform ID |
GPL17639 |
| Series (2) |
| GSE83800 |
small RNA profiling of WT, ros1-4, nrpd1 single mutants and ros1-4/nrpd1doubble mutant [small RNA-seq] |
| GSE83802 |
The DNA demethylase ROS1 targets genomic regions with distinct chromatin modifications |
|
| Relations |
| BioSample |
SAMN05300520 |
| SRA |
SRX1881705 |
