|
Status |
Public on Nov 01, 2016 |
Title |
ros1nrpd1_rep1_sRNA-Seq |
Sample type |
SRA |
|
|
Source name |
ros1nrpd1_sRNA-Seq
|
Organism |
Arabidopsis thaliana |
Characteristics |
genotype/variation: ros1/nrpd1 double 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 |
SAMN05300524 |
SRA |
SRX1881709 |