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Status |
Public on Jul 14, 2016 |
Title |
TV-22 (6268) |
Sample type |
SRA |
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Source name |
leaf
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Organism |
Arabidopsis thaliana |
Characteristics |
cultivar: TV-22 ecotype id: 6268 tissue: leaf
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Extracted molecule |
genomic DNA |
Extraction protocol |
DNA was isolated using a Qiagen Plant DNeasy kit (Qiagen, Valencia, CA) following the manufacturer’s recommendations. Approximately one to three micrograms of genomic DNA was sonicated to ~100 bp using the Covaris S2 System using the following parameters: cycle number = 6, duty cycle = 20%, intensity = 5, cycles/burst = 200 and time = 60 seconds. Sonicated DNA was purified using Qiagen DNeasy minielute columns (Qiagen). Each sequencing library was constructed similar to genomic DNA libraries except the ligation was performed with methylated adapters provided by Illumina. Ligation products were purified with AMPure XP beads (Beckman) at a ratio of 1.8X of beads to sample. Up to 450 ng of ligated DNA was bisulfite treated using the MethylCode Kit (Invitrogen, Carlsbad, CA) following the manufacturer’s guidelines and then PCR amplified using Pfu Cx Turbo (Agilent, Santa Clara, CA) using the following PCR conditions (2 minutes at 95C, 4 cycles of 15 seconds at 98C, 30 seconds at 60C, 4 minutes at 72C and 10 minutes at 72C).
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Library strategy |
Bisulfite-Seq |
Library source |
genomic |
Library selection |
RANDOM |
Instrument model |
Illumina Genome Analyzer IIx |
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Data processing |
Methylated cytosine calls were made using the pipeline described in Lister et al. Human DNA methylomes at base resolution show widespread epigenomic differences. 2009. Nature Genome_build: TAIR10 Supplementary_files_format_and_content: Tab separated file of methylated cytosine positions
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Submission date |
Mar 26, 2016 |
Last update date |
May 29, 2019 |
Contact name |
Joseph R Ecker |
E-mail(s) |
ecker@salk.edu
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Phone |
8584534100
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Organization name |
HHMI-Salk-Institute
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Department |
Genomic Analysis Laboratory
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Lab |
Ecker lab
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Street address |
10010 North Torrey Pines Road
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City |
La Jolla |
State/province |
CA |
ZIP/Postal code |
92037 |
Country |
USA |
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Platform ID |
GPL11221 |
Series (1) |
GSE43857 |
Patterns of Population Epigenomic Diversity in Arabidopsis thaliana (Methyl-Seq) |
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Relations |
BioSample |
SAMN04581357 |
SRA |
SRX1664566 |
Supplementary file |
Size |
Download |
File type/resource |
GSM2099220_allc_6268.tsv.gz |
155.1 Mb |
(ftp)(http) |
TSV |
SRA Run Selector |
Raw data are available in SRA |
Processed data provided as supplementary file |
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