MACE TSS Track Settings
 
TSS Identified by 5' Massive Amplification of cDNA Ends (5' MACE)   (All Expression and Regulation tracks)

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Description

These tracks show the transcription start sites identified by 5' Massive Amplification of cDNA Ends (5' MACE) in D. melanogaster S2-DRSC cells and 0-16 hour embryos. The MACE datasets were obtained from the NCBI Gene Expression Omnibus database under the accession number GSE24521.

Methods

Each dataset was mapped to the D. melanogaster release 6 assembly using bwa with default parameters. The alignment results were analyzed by CAGEr. The tag counts were normalized by the normalizeTagCount function in CAGEr with the following parameters:

method = "powerLaw", fitInRange = c(10, 1000), alpha = 1.05, T = 2*10^6

References

Enderle D, Beisel C, Stadler MB, Gerstung M, Athri P, Paro R. Polycomb preferentially targets stalled promoters of coding and noncoding transcripts. Genome Res. 2011 Feb;21(2):216-26.

Haberle V, Forrest AR, Hayashizaki Y, Carninci P, Lenhard B. CAGEr: precise TSS data retrieval and high-resolution promoterome mining for integrative analyses. Nucleic Acids Res. 2015 Apr 30;43(8):e51.