NCBI Logo
GEO Logo
   NCBI > GEO > Accession DisplayHelp Not logged in | LoginHelp
GEO help: Mouse over screen elements for information.
          Go
Sample GSM2328544 Query DataSets for GSM2328544
Status Public on Sep 27, 2016
Title MNF-Pot-21 (1853)
Sample type SRA
 
Source name leaf
Organism Arabidopsis thaliana
Characteristics cultivar: MNF-Pot-21
ecotype id: 1853
tissue: leaf
Extracted molecule genomic DNA
Extraction protocol Genomic DNA was extracted using the DNeasy Plant Kit (Qiagen, Valencia, CA) from ground, frozen 10 rosette leaves, harvested just before bolting.
Two µg of genomic DNA was fragmented with a Covaris S2 (Covaris, Woburn, MA) to 200 bp, followed by end repair (End-It, Epicenter) and addition of a 3’ A base (Klenow (3'->5' exo-), dA-tailing buffer (NEB)). Cytosine-methylated adapters provided by Bio
 
Library strategy Bisulfite-Seq
Library source genomic
Library selection RANDOM
Instrument model Illumina HiSeq 2500
 
Data processing Map Bisulfite-seq reads to converted Arabidopsis genome by using bowtie 2.0.
Remove clonal reads and Call un-converted C position
Genome_build: TAIR 10 conversion (C-T,G-A)
Supplementary_files_format_and_content: tab delimited file with chromosome, position, strain, mC, h, and sum
 
Submission date Sep 26, 2016
Last update date May 29, 2019
Contact name Joseph R Ecker
E-mail(s) ecker@salk.edu
Phone 8584534100
Organization name HHMI-Salk-Institute
Department Genomic Analysis Laboratory
Lab Ecker lab
Street address 10010 North Torrey Pines Road
City La Jolla
State/province CA
ZIP/Postal code 92037
Country USA
 
Platform ID GPL17639
Series (1)
GSE43857 Patterns of Population Epigenomic Diversity in Arabidopsis thaliana (Methyl-Seq)
Relations
BioSample SAMN05826335
SRA SRX2190721

Supplementary file Size Download File type/resource
GSM2328544_allc_1853.tsv.gz 115.5 Mb (ftp)(http) TSV
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file

| NLM | NIH | GEO Help | Disclaimer | Accessibility |
NCBI Home NCBI Search NCBI SiteMap