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Sample GSM2218937 Query DataSets for GSM2218937
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

Supplementary file Size Download File type/resource
GSM2218937_ros1nrpd1_rep1.bedgraph.gz 4.4 Mb (ftp)(http) BEDGRAPH
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file

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