GEO Logo
   NCBI > GEO > Accession DisplayHelp Not logged in | LoginHelp
GEO help: Mouse over screen elements for information.
Sample GSM1312227 Query DataSets for GSM1312227
Status Public on Mar 28, 2015
Title 9353_10C
Sample type SRA
Source name aerial seedling
Organism Arabidopsis thaliana
Characteristics accession number: 9353
accession name: Död 3
growth temperature: 10C
tissue: whole rosette
developmental stage: 9-true -leaf stage
Growth protocol Accessions were sown on soil and stratified for 3 days at 4 C in the dark. They were then transferred to environmentally controlled growth chambers set at 10C or 16C under long day conditions (04:00-20:00) and individual seedlings were transplanted to single pots after one week. When plants attained the 9-true -leaf stage of development, whole rosettes were collected between 15:00 and 16:00 hours and flash frozen in liquid nitrogen.
Extracted molecule genomic DNA
Extraction protocol For each sample two individual plants were pooled and total DNA was extracted using CTAB and phenol-chloroform
Approximately two micrograms of genomic DNA was sent for BS-seq library construction and sequencing (preformed under contract by Beijing Genomics Institute)
Library strategy Bisulfite-Seq
Library source genomic
Library selection RANDOM
Instrument model Illumina HiSeq 2000
Data processing base calling and de-muiltiplexing done under contract by Beijing Genomics Institute
Reads were aligned to the pseudo-reference genome (TAIR10 with the SNPs from the relevent accession) using using NexGenMap version 0.4.3 with the following settings -p -i 0.90 -R 45 --bs-mapping --silent-clip
Genome_build: TAIR10 (incorporating relevant SNV's)
Supplementary_files_format_and_content: A TSV (tab separated values) detailing the methylation levels at each cytosine was generated using the script from the BSMAP (version 2.73) using the -z and -u flags
Submission date Jan 22, 2014
Last update date May 15, 2019
Contact name Manu Dubin
Organization name Gregor Mendel Institute, Austrian Academy of Sciences
Street address Dr. Bohr-Gasse 3
City Vienna
ZIP/Postal code 1030
Country Austria
Platform ID GPL13222
Series (1)
GSE54292 DNA methylation variation in Arabidopsis has a genetic basis and appears to be involved in local adaptation
BioSample SAMN02594595
SRA SRX446111

Supplementary file Size Download File type/resource
GSM1312227_9353_10C.txt.gz 327.0 Mb (ftp)(http) TXT
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