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Status |
Public on Jan 04, 2017 |
Title |
ibm11_Ler_1st |
Sample type |
SRA |
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Source name |
rosette leaves
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Organism |
Arabidopsis thaliana |
Characteristics |
ecotype: Ler-0 tissue: rosette leaves age: 3 weeks
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Growth protocol |
Plants were grown in plates under long-day conditions (21°C, 16 h light, 8 h dark)
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Extracted molecule |
genomic DNA |
Extraction protocol |
Genomic DNA was extracted using the Plant DNeasy kit (Qiagen) following the manufacturer's instructions. Libraries were constructed starting from 150 ng of genomic DNA, using the EZ-DNA Methylation-Gold Kit (Zymo Research), following by DNA library preparation with the TruSeq DNA methylation kit (Illumina), according to manufacturer's instructions.
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Library strategy |
Bisulfite-Seq |
Library source |
genomic |
Library selection |
RANDOM |
Instrument model |
Illumina NextSeq 500 |
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Description |
ibm1-1 mutant 1st generation
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Data processing |
The raw reads were trimmed using Trimmomatic (Bolger et al, 2014 Bioinformatics) in order to remove adapter sequences. Reads with an average quality value of at least 15 in a window of 4 nucleotides were trimmed from both ends. After trimming, reads shorter than 16 bases were discarded. The remaining sequences were aligned using Bismark (Krueger et al. 2011, Bioinformatics) against the Arabidopsis thaliana genome TAIR10 version or the PacBio Ler-0 genome assembly (http://www.pacb.com/uncategorized/new-data-release-arabidopsis-assembly/) for Col-0 ibm1 or Ler-0 ibm1 mutant, respectively. Duplicated reads were collapsed into one read. Chloroplast sequences were used to estimate the bisulfite conversion. Genome_build: Arabidopsis thaliana Col-0: TAIR10; Ler-0: PacBio assembly (http://www.pacb.com/uncategorized/new-data-release-arabidopsis-assembly/) Supplementary_files_format_and_content: For each genotype, the CX_Report generated by Bismark is reported (Krueger et al. 2011, Bioinformatics).
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Submission date |
Nov 16, 2016 |
Last update date |
May 15, 2019 |
Contact name |
Marco Catoni |
Organization name |
University of Birmingham
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Department |
School of Biosciences
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Street address |
Edgbaston
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City |
Birmingham |
ZIP/Postal code |
B15 2TT |
Country |
United Kingdom |
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Platform ID |
GPL19580 |
Series (1) |
GSE89913 |
Cytosine methylation at CpCpG sites triggers accumulation of non-CpG methylation in gene bodies |
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Relations |
BioSample |
SAMN06020411 |
SRA |
SRX2352823 |
Supplementary file |
Size |
Download |
File type/resource |
GSM2393135_ibm11_Ler_1st.CXreport.txt.gz |
226.9 Mb |
(ftp)(http) |
TXT |
SRA Run Selector |
Raw data are available in SRA |
Processed data provided as supplementary file |
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