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GEO help: Mouse over screen elements for information. |
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| Status |
Public on Jan 11, 2013 |
| Title |
bru1 BS-seq |
| Sample type |
SRA |
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| Source name |
3wk-old leaf tissue
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| Organism |
Arabidopsis thaliana |
| Characteristics |
genotype: bru1
ecotype: Columbia
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| Treatment protocol |
Genomic DNA was extracted using Qiagen DNeasy Mini Kit.
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| Extracted molecule |
genomic DNA |
| Extraction protocol |
Fragmented genomic DNA library as described in Cokus et al., Nature 2008, except directly with pre-methylated final adapters (see Feng et al., Methods Mol. Biol. 2011;733:223-38 for further information)
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| Library strategy |
Bisulfite-Seq |
| Library source |
genomic |
| Library selection |
RANDOM |
| Instrument model |
Illumina HiSeq 2000 |
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| Data processing |
BS-Seq reads were mapped with BS seeker (Chen et al., 2010 BMC Bioinformatics) to TAIR10 chr1..5/C/M, allowing up to 2 mismatches and retaining only uniquely-mapping reads. Identical reads were collapsed into single reads. Only reference genome cytosines covered with at least 4 reads were considered for analysis.
Genome_build: TAIR10
Supplementary_files_format_and_content: Presented as a single base-pair resolution UCSC genome browser wiggle file for each nuclear genome (1-5), where column 1 is the genomic coordinate of the cytosine and column 2 is the methylation level #C/(#C+#T).
Supplementary_files_format_and_content: For each genotype, three wiggle files were generated. Where each file represents data of methylation levels in three sequence contexts (CG, CHG, CHH)
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| Submission date |
Aug 06, 2012 |
| Last update date |
May 15, 2019 |
| Contact name |
Hume Stroud |
| Organization name |
UT Southwestern
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| Street address |
5323 Harry Hines Blvd
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| City |
Dallas |
| State/province |
TX |
| ZIP/Postal code |
75390 |
| Country |
USA |
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| Platform ID |
GPL13222 |
| Series (1) |
| GSE39901 |
Comprehensive analysis of silencing mutants reveals complex regulation of the Arabidopsis methylome. |
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| Relations |
| SRA |
SRX174216 |
| BioSample |
SAMN01103723 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSM980999_bru1_CG.wig.gz |
17.3 Mb |
(ftp)(http) |
WIG |
| GSM980999_bru1_CHG.wig.gz |
17.3 Mb |
(ftp)(http) |
WIG |
| GSM980999_bru1_CHH.wig.gz |
70.6 Mb |
(ftp)(http) |
WIG |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data provided as supplementary file |
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