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Status |
Public on Sep 01, 2014 |
Title |
CVL39 Selected sample D5 bisulfite |
Sample type |
SRA |
|
|
Source name |
CVL39 Selected sample
|
Organism |
Arabidopsis thaliana |
Characteristics |
genotype: Recombinant inbred line CVL39 tissue: Whole above ground plant age: 25 days
|
Treatment protocol |
Library prepared DNA was subjected to bisulfite treatment to convert unmethylated cytosines to thymines for bisulfite sequencing.
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Growth protocol |
Sterilized seeds were initially sown on MA agar plates and stratified at 4°C for three days to ensure synchronised germination. After 12 days seedlings of CVL39 and CVL125 were transferred to pots in a general soil mix and grown under long-day conditions (23°C, 16 h light, 8 h dark). On day 25 the above ground parts of one individual were harvested in an Eppendorf tube containing glass beads and flash frozen in liquid nitrogen for DNA extraction.
|
Extracted molecule |
genomic DNA |
Extraction protocol |
Using four micrograms of genomic DNA, a SOLIDTM fragment library for bisulfite genomic methylation profiling was prepared according to the manufacturer’s instructions Life technologiesTM with the following modifications. Both the P1-A and the P2-A adaptors consisted of 5-methyl-cytosines instead of cytosine, which ensures amplification of both the sense and antisense strands during emulsion PCR and avoids loss of unique molecules. After adaptor ligation and nick-translation, 500 ng of DNA was subjected to bisulfite conversion.
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Library strategy |
Bisulfite-Seq |
Library source |
genomic |
Library selection |
RANDOM |
Instrument model |
AB SOLiD System 3.0 |
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|
Description |
DNA methylome of 25-day-old plants which experienced 5 generations of selection and 2 generations without selection
|
Data processing |
SOCS V1.0 Alignment (Ondov et. al 2010, Bioinformatics, Volume 26, Issue 15, pages 1901-2), using recombinant genomes between Cvi/Ler Ecotypes SOCS V1.0 Alignment gives the methylation statistics as number methylated and unmethylated cytosines per genomic position Filter out positions which are covered by at least 4 and less than 50 reads Apply Fisher's exact test to identify differentially methylated positions between the test samples (S2 samples) and the reference samples (A2 sample) for each genotype (_DMC4 Processed Data Files) Genome_build: Arabidopsis TAIR10
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|
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Submission date |
Mar 27, 2012 |
Last update date |
May 15, 2019 |
Contact name |
Christian Heichinger |
E-mail(s) |
christian.heichinger@uzh.ch
|
Phone |
41-(0)44-634 8275
|
Organization name |
Zürich University
|
Department |
Institute of Plant Biology
|
Lab |
Developmental Genetics
|
Street address |
Zollikerstrasse 107
|
City |
Zürich |
State/province |
Zürich |
ZIP/Postal code |
8008 |
Country |
Switzerland |
|
|
Platform ID |
GPL10088 |
Series (2) |
GSE36845 |
Selection of epigenetic variation in Arabidopsis [Bisulfite-Seq] |
GSE36846 |
Selection of epigenetic variation in Arabidopsis |
|
Relations |
SRA |
SRX131922 |
BioSample |
SAMN00839775 |