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| Status |
Public on May 03, 2012 |
| Title |
crt1-4 bisulfite |
| Sample type |
SRA |
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| Source name |
leaf tissue, crt1-4, bisulfite-treated genomic DNA
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| Organism |
Arabidopsis thaliana |
| Characteristics |
genotype: crt1-4 (eco. Columbia)
tissue: leaf
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| Extracted molecule |
genomic DNA |
| Extraction protocol |
Genomic DNA isolated by phenol/chloroform and bisulfite treated.
Converted and fragmented genomic DNA library as described in Cokus et al., Nature 2008 (PMID 18278030), except directly with pre-methylated final adapters (see Feng et al., Methods Mol. Biol. 2011;733:223-38 (PMID 21431774) 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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| Description |
Bisulfite-treated genomic DNA.
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| Data processing |
BS-Seq reads were mapped with BS seeker (Chen et al., 2010 BMC Bioinformatics (PMID 20416082)) to TAIR8 chr1..5/C/M, allowing up to 2 mismatches and retaining only uniquely-mapping reads. Only reference genome cytosines covered with at least 4 reads were considered for analysis.
Supplementary_files_format_and_content: Each processed file is tab-delimited plain text with five columns and UNIX-style line endings. Lines enumerate a subset of TAIR8 chr1..5 genomic cytosines (ordered by ascending column 1 chromosome number, breaking ties by ascending column 2 coordinate). Column 1 is chromosome (1..5). Column 2 is 1-based coordinate of the genomic cytosine (successive reference + strand bases are 1, 2, 3, ... and each - strand base is numbered by the + strand base with which it is paired). Column 3 is context (CG, CHG, or CHH) of the genomic cytosine. Column 4 is genomic strand (+ or -) of the genomic cytosine. Column 5 is the empirical observed fraction of 5'-methylation, calculated as (# read C) / (# read C + # read T).
Supplementary_files_format_and_content: Quality scores in _qseq files are Phred scale with +64 ASCII offset... non-multiplexed: 1 lane.
Genome_build: TAIR8
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| Submission date |
May 01, 2012 |
| Last update date |
May 15, 2019 |
| Contact name |
Shawn J. Cokus |
| Organization name |
UCLA
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| Street address |
UCLA, 3000 Terasaki Life Sciences Building, 610 Charles Young Drive East
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| City |
Los Angeles |
| State/province |
CA |
| ZIP/Postal code |
90095 |
| Country |
USA |
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| Platform ID |
GPL13222 |
| Series (1) |
| GSE37644 |
MORC family ATPases required for heterochromatin condensation and gene silencing |
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| Relations |
| SRA |
SRX145426 |
| BioSample |
SAMN00990551 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSM925657_crt1-4_BSseq_processed.enumerationOfSubsetOfAthTAIR8genomicCs--chr12345-1basedCoord-CG_CHG_CHH-strand-fraction5methylC.txt.gz |
130.7 Mb |
(ftp)(http) |
TXT |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data provided as supplementary file |
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