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Revision as of 23:37, 16 March 2013 by Imhenry (Talk | contribs)

Rice CHIP-Seq Sequence Files

  • Please find below all of our CHIP-Seq data. All reads will also be deposited to the GEO database as soon as we have a complete set of tables to complement the reads (peak files, gene location etc.).
  • Legend:
N : O. sativa, var. Nipponbare
K: O. sativa, var. Kasalath
9: O. sativa, var. 93-11
  • Sample collection:
Each individual sample corresponds to the aerial portion of 20 seedlings, harvested at 4 days after germination and flash-frozen in liquid nitrogen. The twenty seedlings were pooled and chromatin was extracted. For each genotype, two independent biological replicates were processed. For each biological replicate, chromatin was divided into three for the following sample types: input chromatin, H3K27me3 CHIP and H3K4me3 CHIP.
  • Bioinformatics:
- Files denoted with a "*" were processed by Illumina's CASAVA 1.8 pipeline. Therefore sequence qualities are already in sanger format. All other files contain quality scores in Illumina format

- Checksum are indicated as a way to insure that the file downloaded is an exact replicate of the file posted on our server. This helps ensure the download is complete and did not generate any error. The checksums provided below correspond to the uncompressed version of the file. To obtain the checksum please run one of the following commands (please note for large files this might take a little bit longer):
- For Mac Os X, please run the following command in the terminal: "md5 filename" where filename is the name of the file you want to know the checksum
- For Linux, please run the following command in the terminal: "md5sum filename" where filename is the name of the file you want to know the checksum
  • Please do not hesitate to contact us with any question email


Sample Genotypes Read Length Sequence File Link File Checksum
K4-1
K4-2
K27-1
K7-2
Input 1
Input 2
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