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Sample GSM2323849 Query DataSets for GSM2323849
Status Public on Dec 13, 2016
Title WT_Vegetative
Sample type SRA
 
Source name isolated nuclei from pollen
Organism Arabidopsis thaliana
Characteristics genotype: wildtype
nuclei type: vegetative
ecotype: Col-0
Growth protocol A. thaliana plants were grown under 16h light/ 8h dark in a growth chamber (21°C, 70% humidity)
Extracted molecule genomic DNA
Extraction protocol Sperm and vegetative nuclei were isolated by FACS as previously described (1). DNA was extracted with ChargeSwitch kit following the manufacturer’s instructions. Reference: 1. Ibarra CA, et al. (2012) Active DNA demethylation in plant companion cells reinforces transposon methylation in gametes. Science 337:1360-1364.
Libraries were prepared with Ovation Ultralow Methyl Seq kit following the manufacturer’s instructions.
 
Library strategy Bisulfite-Seq
Library source genomic
Library selection RANDOM
Instrument model Illumina HiSeq 2000
 
Data processing Bisulfite-Seq: We used Perl scripts to convert all the Cs in the reads (and in the scaffolds) to Ts, and aligned the converted reads to the converted reference scaffold, allowing up to two mismatches per read. 76 base reads were divided into the first 45 and the last 31 bases, 100 base reads and 150 base reads were divided in half. Each half of the read was aligned independently using bowtie, allowing up to two mismatches. The coordinates of the two halves were subsequently correlated; the second half was discarded if it did not match the first.
Single_C: We used Perl scripts to recover the original sequence of each mapped read and, for each C (on either strand), count the number of times it was sequenced as a C or a T.
50bp_window: We used a Perl script to calculate fractional methylation (#C/(#C+#T)) within a 50 bp sliding window for each sequence context (CG, CHG, CHH).
Genome_build: TAIR10
Supplementary_files_format_and_content: All files are in GFF format. Files contain fractional methylation data either for individual cytosines (single-c) or in 50 bp windows.
 
Submission date Sep 21, 2016
Last update date May 15, 2019
Contact name Xiaoqi Feng
E-mail(s) xiaoqi.feng@jic.ac.uk
Organization name John Innes Centre
Department Cell and Developmental Biology
Lab Xiaoqi Feng
Street address Norwich Research Park
City Norwich
State/province Norfolk
ZIP/Postal code NR4 7UH
Country United Kingdom
 
Platform ID GPL13222
Series (1)
GSE87170 DNA methylation inheritance across generations
Relations
BioSample SAMN05792882
SRA SRX2182207

Supplementary file Size Download File type/resource
GSM2323849_WT.veg.CG.tair10.gff.gz 40.1 Mb (ftp)(http) GFF
GSM2323849_WT.veg.CG.tair10.w50.gff.gz 14.0 Mb (ftp)(http) GFF
GSM2323849_WT.veg.CHG.tair10.gff.gz 43.2 Mb (ftp)(http) GFF
GSM2323849_WT.veg.CHG.tair10.w50.gff.gz 15.7 Mb (ftp)(http) GFF
GSM2323849_WT.veg.CHH.tair10.gff.gz 201.4 Mb (ftp)(http) GFF
GSM2323849_WT.veg.CHH.tair10.w50.gff.gz 23.8 Mb (ftp)(http) GFF
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file

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