|
| Status |
Public on Feb 03, 2015 |
| Title |
Al_MeDIP_rep2 |
| Sample type |
SRA |
| |
|
| Source name |
young leaves
|
| Organism |
Arabidopsis lyrata |
| Characteristics |
strain: MN47
chip antibody: 5mC (Diagenode,Mab-006, lot.#DA-0015)
tissue: young leaves
|
| Growth protocol |
Plants of Arabidopsis lyrata accession MN47 were grown in soil under long day conditions (16h light/8h dark) at 22.5C.
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
Chromatin and DNA immunoprecipitation was performed essentially as described in Gendrel et al., 2005 and Cortijo et al., 2014, respectively. Total RNA was extracted using RNeasy Mini Kit (Qiagen) according to manufacturers instructions and its quality was validated using RNA 6000 NanoChip (Agilent).
20 ng of immunoprecipitated (IP) and genomic (INPUT) DNA and 1 ug of total RNA were used to prepare libraries with the ChIP-Seq DNA Sample Prep Kit IP-102-1001 and TruSeq RNA Sample Prep Kit v2 RS-122-2002 (Illumina), respectively. Quality of libraries was validated using 2100 Bioanalyzer (Agilent). Libraries were sequenced with Illumina Genome Analyzer IIx according to manufacturers instructions.
|
| |
|
| Library strategy |
MeDIP-Seq |
| Library source |
genomic |
| Library selection |
5-methylcytidine antibody |
| Instrument model |
Illumina Genome Analyzer IIx |
| |
|
| Data processing |
Basecalls performed using SHORE v0.7alpha3.
Quality filtering included trimming of low quality nucleotides.
ChIP-seq, MeDIP-seq and RNA-seq reads were mapped against the Arabidopsis lyrata reference using Bowtie choosing one match in case of multiple ones and allowing one mismatch.
For the ChIP-seq and MeDIP-seq libraries, since average read coverage was highly correlated between the two biological replicates, they were pooled for subsequent analysis. In order to reduce biases introduced by PCR amplification, a maximum of 5 reads mapping at exactly the same positions were taken into account.
Peak detection was done using SICER normalising the ChIP-seq coverage by the INPUT coverage. Window size was adjusted according to the distribution of the mark over the genes: 150 bp for H3K4me3 and 300 bp for H3K27me3. Effective genome size was estimated as 85% of the total genome and FDR set at 10−3 .
mRNA abundance for each gene was estimated as the average number of positions mapped to its transcribed region over the total number of positions covered.
Genome_build: Arabidopsis lyrata
Supplementary_files_format_and_content: bedGraph = scores represent the ChIP-seq and MeDIP-seq coverage ; bed = scores represent number of reads per domain ; covexonsByGene.txt = mRNA abundance per gene
|
| |
|
| Submission date |
Feb 06, 2014 |
| Last update date |
May 15, 2019 |
| Contact name |
François ROUDIER |
| E-mail(s) |
francois.roudier@ens-lyon.fr
|
| Organization name |
Ecole Normale Supérieure de Lyon
|
| Department |
Biologie
|
| Lab |
RDP
|
| Street address |
46 Allée d'Italie
|
| City |
Lyon |
| ZIP/Postal code |
69364 |
| Country |
France |
| |
|
| Platform ID |
GPL16940 |
| Series (2) |
| GSE54727 |
Genome-wide profiling of H3K4me3, H3K27me3 H3K27me1 and 5mC enrichment and mRNA levels in young leaves of Arabidopsis lyrata |
| GSE54728 |
Genome expansion of Arabis alpina linked with retrotransposition and reduced symmetric DNA methylation |
|
| Relations |
| BioSample |
SAMN02629993 |
| SRA |
SRX466004 |
