|
| Status |
Public on Aug 17, 2016 |
| Title |
Col |
| 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 |
genomic DNA |
| Extraction protocol |
Genomic DNA was prepared using the Macherey Nagel plant DNA extraction kit
Library construction protocol: According to BGI company
|
| |
|
| Library strategy |
Bisulfite-Seq |
| Library source |
genomic |
| Library selection |
RANDOM |
| Instrument model |
Illumina Genome Analyzer |
| |
|
| Data processing |
Quality control using FastQC and adapter removal using Cutadapt. Short reads (<20 bp) were removed Trim Galore
Mapping : BISMARK (1 MM) Bowtie 2.0 unique mapping,Giving unmapped reads / ambiguous reads. Deduplication script provided by BISMARK to delete PCR biais
Methylation information : Methylation extraction script provided by BISMARK
Filtering : Coverage filter (<100). Windows : 100 bp consecutive windows. Methaltion levels expressed as percent of methylted readfs over totla reads. Difference between identical windows (same start same stop). Apply a Fisher test with a filtering value p<0.01 and difference >40% for CG and >10% for CHG and CHH
DMRs were called in joined windows as same direction (hyper DMR and hypo DMR allowing 1 window gap). Filtering for less that 4 C
Genome_build: TAIR10
Supplementary_files_format_and_content: gff files
|
| |
|
| 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) |
| GSE76648 |
Global Genome Repair factors are essential for shaping the DNA methylation landscape in Arabidopsis [BS-seq] |
| GSE76651 |
Global Genome Repair factors are essential for shaping the DNA methylation landscape in Arabidopsis |
|
| Relations |
| BioSample |
SAMN04388522 |
| SRA |
SRX1521984 |
