|
| Status |
Public on Sep 01, 2014 |
| Title |
CVL125 Selected sample D6 bisulfite |
| Sample type |
SRA |
| |
|
| Source name |
CVL125 Selected sample
|
| Organism |
Arabidopsis thaliana |
| Characteristics |
genotype: Recombinant inbred line CVL125
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.
|
| 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.
|
| |
|
| Library strategy |
Bisulfite-Seq |
| Library source |
genomic |
| Library selection |
RANDOM |
| Instrument model |
AB SOLiD System 3.0 |
| |
|
| 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
|
| |
|
| 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 |
SRX131927 |
| BioSample |
SAMN00839780 |
