DBTSS6, TSS database from full-length cDNAs and Solexatags

Description

DBTSS (DataBase of Transcriptional Start Sites) represents exact positions of transcriptional start sites (TSSs) in the genome based on a full length cDNA collection and a unique experimentally validated TSS sequencing method, TSS Seq.

Source

Solexa Tag Data were downloaded from: DBTSS6
Input file format: Tab-dlimited TXT

Samples

From H. sapiens (March 2006 NCBI36/hg18).

	Filename	Description	Feature	GEO-ID
1	DBTSS6_cDNA.sga	DBTSS from cDNA	DBTSS	-
2	DBTSS6_hek293_solexatag.sga	DBTSS from Solexa, hek293 cells	DBTSS	-
3	DBTSS6_mcf7_solexatag.sga	DBTSS from Solexa, mcf7 cells	DBTSS	-

Technical Notes

The source files are the following:

hsonepass.tab.gz: Human tissues full-length cDNA mapping data;
hs_mcf7_solexatag.tab.gz: Human mcf7 Solexa tag mapping data;
hs_hek293_solexatag.tab.gz: Human hek293 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

Wakaguri H, Yamashita R, Suzuki Y, Sugano S, Nakai K
DBTSS: database of transcription start sites, progress report 2008. Nucleic Acids Res. 2008 Jan;36(Database issue):D97-101. Epub 2007 Oct 16. PMID: 17942421

Genome browser viewable files

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