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Sample GSM3403465 Query DataSets for GSM3403465
Status Public on Nov 22, 2018
Title epi12
Sample type SRA
 
Source name whole seedling
Organism Arabidopsis thaliana
Characteristics ecotype: Col-0
tissue: seedling
age: 2 weeks
line: met1-3 derived epiRIL epi12 F9
Growth protocol Arabidopsis epiRIL seeds were sown on ½ x MS (Plant) medium plates and grown for 14 days under Long day light conditions (16h of light).
Extracted molecule genomic DNA
Extraction protocol Approximately 10 seedlings were harvested per epiRIL for ~100mg tissue from which DNA was extracted using the Qiagen DNeasy Plant Mini Kit, following the manufacturer’s instructions (Qiagen N.V., Hilden, Germany).
Before library preparation, DNA was fragmented to an average insert size of 350bp using 24 cycles of 30 seconds each on a Bioruptor® Diagenode sonication device. The genomic DNA sequencing libraries for the Arabidopsis epiRILs were prepared using the TruSeq DNA PCR-Free LT Library Prep Kit following the manufacturer’s instructions (Illumina, San Diego, CA), starting from 1.1µg of sonicated DNA. Libraries were validated using the High Sensitivity D1000 screentape on the 2200 Tapestation instrument (Agilent technologies, Santa Clara, CA) and the LightCycler® 480 Instrument II using the LightCycler® 480 SYBR Green I Master mix (Roche, Basel, Switzerland).
 
Library strategy OTHER
Library source genomic
Library selection other
Instrument model Illumina NextSeq 500
 
Data processing Library strategy: DNA-Seq
The raw reads were trimmed using Trimmomatic to remove adapter sequences. Reads with an averaged value of at least 15 in a 4 nucleotide window were trimmed from both ends. After trimming, reads pairs with at least one mate shorter that 36 bp were discarded.
The remaining reads were aligned with bowtie2 (Langmead and Salzberg, 2012) with the –no mixed and –non deterministic option, against the reference TAIR10 Arabidopsis genome (www.arabidopsis.org).
Genome coverage was calculated for each genome position using genomecov (bedtools v2.26.0) and normalized to Arabidopsis genome and library size. Arabidopsis genomic regions with a coverage of more than 2.5 fold or less than 0.2 fold of the average genome coverage in the Col-0 wild type control were masked, to avoid to call peaks in regions with high copy number or not enough covered (e.g. plastids DNA insertion, ribosomal repeats, microsatellites).
Peak call was done for each epiRILs mapped bam file in comparison to the Col-0 control condition with macs2 (https://github.com/taoliu/MACS/), setting the fragment size to 75 and extended size to 400 bp, and the options –B, -SPMR and –no model, and using a Columbia-0 sample as control.
The Log based background subtraction was performed with macs2 bdgcmp with “logLR” as model and a p-value threshold of 0.00001.
Genome_build: TAIR10
Supplementary_files_format_and_content: Processed data files contain list of peaks from macs2 output, in xls format
 
Submission date Sep 27, 2018
Last update date Nov 22, 2018
Contact name Marco Catoni
Organization name University of Birmingham
Department School of Biosciences
Street address Edgbaston
City Birmingham
ZIP/Postal code B15 2TT
Country United Kingdom
 
Platform ID GPL19580
Series (1)
GSE120571 Mobilization of Pack-CACTA transposons in Arabidopsis suggests the mechanism of gene shuffling
Relations
BioSample SAMN10138117
SRA SRX4745150

Supplementary file Size Download File type/resource
GSM3403465_epi12_peaks.txt.gz 6.3 Kb (ftp)(http) TXT
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file

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