|
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 |