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.

Solexa Tag Data were downloaded from: DBTSS7
Input file format: Tab-delimited TXT

Samples

From M. musculus (July 2007 NCBI37/mm9).

Transcription Profiling data:

	Filename	Description	Feature	GEO-ID
1	dbtss7.sga	DBTSS Mouse	DBTSS	-

Technical Notes

The source files are the following:

3t3_data.tab.gz: Mouse 3T3 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

The source format is a non-standard tab-delimited format that has been converted to SGA via an ad hoc perl script.

References

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/