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| Status |
Public on May 13, 2015 |
| Title |
MA1_3_G18_12_r1 |
| Sample type |
SRA |
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| Source name |
leaf tissue
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| Organism |
Arabidopsis thaliana |
| Characteristics |
cultivar: Col-0
tissue: leaf
age: ~3 week old plants
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| Growth protocol |
Arabidopsis thaliana were grown in long days (16 hours of light) at 24C
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| Extracted molecule |
genomic DNA |
| Extraction protocol |
Genomic DNA (gDNA) was purified from Arabidopsis thalina leaf tissue using a Qiagen DNease Plant Kit (Qiagen, Valencia, CA), according to the manufacturer’s instructions. MethylC-Seq libraries were constructed according to Urich MA, Nery JR, Lister R, Schmitz RJ, Ecker JR. (2014) MethylC-seq: Base resolution whole genome bisulfite sequencing library preparation. Nature Protocols (in press)
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| Library strategy |
Bisulfite-Seq |
| Library source |
genomic |
| Library selection |
RANDOM |
| Instrument model |
Illumina NextSeq 500 |
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| Data processing |
Data were mapped to the Arabidopsis thaliana reference genome version 10 (TAIR10)
MethylC-seq analysis were performed as described in Schmtiz et al. Epigenome-wide inheritance of DNA methylation variants in a recombinant inbred population. Genome Research (2013).
Genome_build: TAIR10
Supplementary_files_format_and_content: MA[pedigreeID]_[experimentID]_G[generationsFromCommonFounder]_[lineNumberID]_r[replicate].txt.gz contains for every cytosine in the TAIR 10 genome: Chromosome, strand, position in the genome, context, methylated coverage and total coverage Uncompressed data is in a tab delimited format. Format, per column: <chr TAIR10> <strand TAIR10> <C position TAIR10> <sequence context of the cytosine> X=CG, Y=CHG and Z=CHH <methylated coverage> <total coverage>
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| Submission date |
Dec 23, 2014 |
| Last update date |
May 15, 2019 |
| Contact name |
Robert J Schmitz |
| E-mail(s) |
schmitz@uga.edu
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| Organization name |
University of Georgia
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| Department |
Genetics
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| Street address |
B416 Davison Life Sciences
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| City |
Athens |
| State/province |
GA |
| ZIP/Postal code |
30602 |
| Country |
USA |
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| Platform ID |
GPL19580 |
| Series (1) |
| GSE64463 |
Rate, spectrum, and evolutionary dynamics of spontaneous epimutations |
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| Relations |
| BioSample |
SAMN03272749 |
| SRA |
SRX835889 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSM1571832_MA1_3_G18_12_r1.txt.gz |
153.1 Mb |
(ftp)(http) |
TXT |
SRA Run Selector |
| Processed data provided as supplementary file |
| Raw data are available in SRA |
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