Gencode, TSS for known genes.

TSS collections from GENCODE versions v24, v28, v47

• Raw data was downloaded from: https://ftp.ebi.ac.uk/pub/databases/gencode/Gencode_human/
• Input file format: GFF3
• Download date: 17-10-2024

From H. sapiens (Dec 2013 GRCh38/hg38).

Genome Annotation:

	Filename	Description	Feature	GEO-ID
1	gencode.v47.hg38.sga	TSS from Gencode v47	TSS	-
2	gencode.v28.hg38.sga	TSS from Gencode v28	ENSEMBL	-
3	gencode.v24.ucsc.hg38.sga	TSS from Gencode v24	ENSEMBL	-

The SGA files were generated from GFF3 format with a custom shell script available from https://epd.expasy.org/ftp/mga/hg38/gencode/scripts/ In the latest version v47, all transcripts with "transcript_support_level=1" and "gene_type=protein_coding" were included.

• Frankish A, Diekhans M, Jungreis I, Lagarde J, Loveland JE et al.
  GENCODE 2021. Nucleic Acids Res. 2021 Jan 8;49(D1):D916-D923. doi: 10.1093/nar/gkaa1087. 33270111