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| Status |
Public on Jan 01, 2014 |
| Title |
MSH1-epiF3, biological rep 1 |
| Sample type |
SRA |
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| Source name |
arieal part, MSH-epiF3
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| Organism |
Arabidopsis thaliana |
| Characteristics |
ecotype: Columbia-0
genotype/variation: MSH1-epiF3
tissue: above ground part - leaves and flower
development stage: Mixed stage
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| Growth protocol |
Plants were grown under 12h light.
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| Extracted molecule |
genomic DNA |
| Extraction protocol |
About 15 ug of gemonic DNA was sonicated to a peak range from 200bp to 600bp, then Phenol/ Chloroform purified and ethanol precipitated. About 12ug of sonicated DNA was treated with Mung Bean Nuclease, then Phenol/Chloroform purified and ethanol precipitated. About 3ug of Mung Bean Nuclease treated genomic DNA was End repaired, 3’ Ends adenylated by using illumine Genomic DNA Samples Prep Kit. The adenylated DNA fragment was then ligated to methylation adapters. Methylation adapted DNA was column purified and ran agarose gel. A fraction of 280bp to 400bp was gel purified by using QIAquick Gel Purification kit. Another 3ug of Mung Nean Nuclease treated genomic DNA was used to repeat the whole process to collect second fraction of 280bp to 400bp methylation adapted DNA. Two methylation adapted fractions were pooled together and subjected to bisulfite treatment MethylEasy Xceed kit according to manufacturer’s instructions (Human Genetics Signature). Three independent library PCR enrichment was done by using 10ul from a total of 30ul bisulfate treated DNA as input template. The PCR reaction mixture were: 10ul DNA, 5ul of 10x pfuTurbo Cx buffer, 0.7ul of PE1.0 primer, 0.7ul PE2.0 primer, 0.5ul of dNTP(25mM), 1ul of PfuTurbo Cx Hotstart DNA Polymerase, and add water to a total volume of 50ul. The PCR parameters were: 95C for 2min, proceeded by 12 cycles of 95C for 30sec, 65C for 30sec and 72C for 1 min, then followed by 72C for 5min. PCR product was column purified respectively and an equal amount of volume from each PCR reaction was pooled together to a final concentration of 10nM. Libraries were then sequenced on the Illumina Genome Analyzer II using three 36-cycle TrueSeq sequencing kits v5 to read 116 nucleotides of sequence from a single end of each insert, by V8 protocols.
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| Library strategy |
Bisulfite-Seq |
| Library source |
genomic |
| Library selection |
RANDOM |
| Instrument model |
Illumina Genome Analyzer II |
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| Description |
enriched nuclear DNA
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| Data processing |
Sequence reads were mapped to the Arabidopsis TAIR10 genome (ftp://ftp.arabidopsis.org/home/tair/Sequences/whole_chromosomes/) with the program Bismark (http://www.bioinformatics.bbsrc.ac.uk/projects/bismark/). One mismatch was allowed in the first 50 nucleotides. Only reads that map to a unique genomic locus were retained. The methylation status of each cytosine in mapped reads were determined by comparing reads to the reference sequence and the context of each cytosine (CpG, CHG, or CHH) was also determined.
Genome Build:
F3_1_bismarkMap.txt: TAIR10
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| Submission date |
Mar 25, 2012 |
| Last update date |
May 15, 2019 |
| Contact name |
Ying-Zhi Xu |
| E-mail(s) |
ying-zhi2@unl.edu
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| Phone |
402-472-6998
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| Organization name |
University of Nebraska
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| Department |
Center for Plant Science Innovation
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| Lab |
Sally Mackenzie
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| Street address |
1901 Vine St.
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| City |
Lincoln |
| State/province |
NE |
| ZIP/Postal code |
68588 |
| Country |
USA |
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| Platform ID |
GPL9302 |
| Series (1) |
| GSE36783 |
High-throughput Illumina sequencing of bisulfite transformed genomic DNA from Arabidopsis thaliana wild-type, msh1 mutant and MSH1-epiF3 lines |
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| Relations |
| SRA |
SRX131542 |
| BioSample |
SAMN00839541 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSM901007_F3_1_bismarkMap.txt.gz |
838.6 Mb |
(ftp)(http) |
TXT |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data provided as supplementary file |
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