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Sample GSM2031995 Query DataSets for GSM2031995
Status Public on Aug 17, 2016
Title Col_smallRNA
Sample type SRA
 
Source name seedlings
Organism Arabidopsis thaliana
Characteristics developemental stage: 10 old days in vitro grown seedling
genotype: WT
tissue: seedling
Growth protocol Ten day old in vitro grown seedlings. MS liquid medium (1.5% sucrose). 16H/8H light/dark photoperiod (21°C/18°C). Roudier et al. EMBO J. (2011)
Extracted molecule total RNA
Extraction protocol Total RNA were prepared using Trizol (Sigma)
Library construction protocol: According to FASTERIS company
 
Library strategy ncRNA-Seq
Library source transcriptomic
Library selection size fractionation
Instrument model Illumina HiSeq 2500
 
Description Col
Data processing basecalling performed by FASTERIS company (HiSeq Control Software 2.0.5 - RTA 1.17.20.0 - CASAVA 1.8.2)
3' adapter removal performed by FASTERIS company
mapping performed on Arabidopsis genome (TAIR10) with bowtie (parameters -t -q -y -e 50 -n 0 -a --best --strata)
filter reads of 24 and 25 nt
overlap with DMR calculated with BEDTools-IntersectBed (parameter -f 0.5) and normalised by read per million
Genome_build: TAIR10
Supplementary_files_format_and_content: gff files contains the DMR of interest and the number of reads (in read per million) of 24-25 nt overlapping this region (score column). The annotation column contain the name of the arabidopsis gene which include this region.
 
Submission date Jan 07, 2016
Last update date May 15, 2019
Contact name Jean Molinier
E-mail(s) Jean.Molinier@ibmp-cnrs.unistra.fr
Phone +33 (0) 3 67 15 53 12
Organization name IBMP-CNRS
Street address 12 rue du General Zimmer
City Strasbourg
ZIP/Postal code 67084
Country France
 
Platform ID GPL17639
Series (2)
GSE76649 Global Genome Repair factors are essential for shaping the DNA methylation landscape in Arabidopsis [small RNA-seq]
GSE76651 Global Genome Repair factors are essential for shaping the DNA methylation landscape in Arabidopsis
Relations
BioSample SAMN04388514
SRA SRX1521979

Supplementary file Size Download File type/resource
GSM2031995_Col-24-nt-CG-hyperDMR-sumTotRPM.gff.gz 1016 b (ftp)(http) GFF
GSM2031995_Col-24-nt-CG-hypoDMR-sumTotRPM.gff.gz 1.4 Kb (ftp)(http) GFF
GSM2031995_Col-24-nt-CHG-hyperDMR-sumTotRPM.gff.gz 23.1 Kb (ftp)(http) GFF
GSM2031995_Col-24-nt-CHG-hypoDMR-sumTotRPM.gff.gz 14.0 Kb (ftp)(http) GFF
GSM2031995_Col-24-nt-CHH-hyperDMR-sumTotRPM.gff.gz 33.4 Kb (ftp)(http) GFF
GSM2031995_Col-24-nt-CHH-hypoDMR-sumTotRPM.gff.gz 14.9 Kb (ftp)(http) GFF
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file

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