DBTSS7, TSS database and full-length cDNAs

Description

DBTSS (DataBase of Transcriptional Start Sites) represents exact positions of transcriptional start sites (TSSs) in the genome based on a unique experimentally validated TSS sequencing method, TSS Seq. DBTSS also integrates newly generated Transcription Profiling data of subcellular- fractionated RNAs and ChIP Seq data of histone modifications, RNA polymerase II and several transcriptional regulatory factors in cultured cell lines. It also includes recently accumulating external epigenomic data, such as chromatin map of the ENCODE project. TSS information is associated with public and original SNV data, in order to indentify single nucleotide variations (SNVs) in the regulatory regions.

Source

Samples

Technical Notes

The source files are the following:

• adult_tissue.tar.gz: Human adult tissues Solexa tag mapping data;
• Beas2B.tar.gz: Human Beas2B Solexa tag mapping data;
• DLD1.tar.gz: Human DLD1 Solexa tag mapping data;
• fetal_tissue.tar.gz: Human fetal tissues Solexa tag mapping data;
• HEK293.tar.gz: Human Hek293 Solexa tag mapping data;
• MCF7.tar.gz: Human MCF7 Solexa tag mapping data;
• Ramos.tar.gz: Human Ramos Solexa tag mapping data;
• TIG.tar.gz: Human TIG Solexa tag mapping data;

The contents of the tab-delimited source files are the following:

• ID (internal unique ID)
• Tag pattern (0=confident 1=not confident)
• Tag type (NM_ correspond,intergenic,anti-sense)
• Group ID (internal ID)
• Refseq Name
• Anti sense refseq name
• Promoter ID
• Alternative promoter ID
• Chromosome
• Strand (1= forward/0= reverse)
• Represent tss position
• Number of tag
• Number of total tag
• TSS Cluster Start
• TSS Cluster End

References

1. Yamashita R, Wakaguri H, Sugano S, Suzuki Y, Nakai K
   DBTSS provides a tissue specific dynamic view of Transcription Start Sites. Nucleic Acids Res. 2010 Jan;38(Database issue):D98-104. Epub 2009. PMID: 19910371

Genome browser viewable files

ftp://ftp.hgc.jp/pub/hgc/db/dbtss/dbtss_ver7/bed_files/