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Sample GSM2640726

Query DataSets for GSM2640726

Status

Public on Jan 01, 2018

Title

PEP1 ChIP-Seq WT rep2

Sample type

SRA

Source name

Pajares above-ground

Organism

Arabis alpina

Characteristics

tissue: above-ground tissue
genotype: Pajares

Treatment protocol

For ChIP on PEP1 we used Pajares and pep1-1 mutant with 1 µl of PEP1 antiserum raised against the C-terminal domain of PEP1 protein. For ChIP on FLC we analysed the Arabidopsis genotypes Col FRI and flc-3 FRI and 2 µl of FLC antiserum was used. Three independent biological replicates were performed for PEP1 ChIP-seq assays and two for FLC ChIP-seq. For ChIP on PEP1 the Pajares and pep1-1 genotypes were used.

Growth protocol

For ChIP experiments plants were grown in LD for 2 weeks and above-ground tissue was collected at ZT8.

Extracted molecule

genomic DNA

Extraction protocol

After crosslinking, the ChIP and the ChIP-seq was done as in Mateos et al. (2015) Genome Biol 16:31, for both species.
For ChIP-seq, 10 μl from the eluted chromatin was then used for library preparation using Ovation Ultralow DR Multi- plex System (NuGen, Leek, The Netherlands). Libraries were sequenced using an Illumina Hi-Seq2500 instrument.

Library strategy

ChIP-Seq

Library source

genomic

Library selection

ChIP

Instrument model

Illumina HiSeq 2500

Data processing

For both species, low quality and duplicated reads in the raw sequencing data were filtered out using Parallel-QC v1.0 (Zhou et al., 2013; PLoS ONE). Low quality reads were considered those not having Phred quality scores≥13 in at least 90% of the bases called. Duplicated reads were also removed to achieve a better specificity (fewer false positive peaks) during the peak-calling step at each individual replicate as recommended in Bailey et al. (2013), PLoS Comput. Biol.
Reads kept were then mapped either to the Arabis alpina reference assembly V3 (Willing et al., 2015; Nature Plants) or to the Arabidopsis thaliana TAIR10 using Bowtie v2.0.2 (Langmead et al., 2019; Genome Biol.), reporting alignments under default mode parameters.
The software PeakRanger (Feng et al., 2011; BMC Bioinformatics) was used to identify read-enriched genomic regions (P-value <1e-6, q-value (FDR) < 0.01, rest of parameters default).
Using MULTOVL v1.2 with parameters '-L 1 -u-m 2 -M 0 -s multovl -f BED' (Aszodi A, 2012; Bioinformatics), a total of 222 peak regions present in at least two replicates of PEP1 ChIP-seq or 377peak regions present in the two replicates of FLC ChIP-seq were retained for further processing (the union of overlapping regions was reported, minimum overlap required 1bp). After filtering by peak length (peaks shorter than 1.5kb were kept), we obtained the final peak set for both species, namely 204 peaks in Arabis alpina and 297 peaks in Arabidopsis thaliana.
Genome_build: TAIR10 (A.thaliana); A_alpina_V3 (A.alpina, http://arabis-alpina.org/refseq.html)

Submission date

May 25, 2017

Last update date

May 15, 2019

Contact name

Julieta Mateos

E-mail(s)

[email protected]

Phone

+054 11 5238-7500

Organization name

Max Planck Institute for Plant Breeding Research