|
| Status |
Public on Aug 17, 2016 |
| Title |
nrpd1a_smallRNA |
| Sample type |
SRA |
| |
|
| Source name |
seedlings
|
| Organism |
Arabidopsis thaliana |
| Characteristics |
developemental stage: 10 old days in vitro grown seedling
genotype: nrpd1a (Salk_583051)
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 Genome Analyzer |
| |
|
| Description |
nrpd1a
|
| 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 |
GPL9062 |
| 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 |
SAMN04388516 |
| SRA |
SRX1521981 |
