Annotation Tracks Mapping Transcription Start Sites' Positions On Xenopus Or Zebrafish

Question

[Anima Mundi]

Hello everybody,

could you please point me out an annotation track mapping transcription start sites' positions on Xenopus tropicalis or zebrafish? I would prefer tracks based on wet-lab experimental evidence, but I also welcome predictions-based tracks.

I have been looking for a previously found Ensembl track mapping predictions of transcription start sites for zebrafish; I remember it was present time ago (months), but now I cannot find it anymore (and, I must admit, I forgot its name).

Thanks in advance.

Answer 1

[Chirag Nepal]

There is a suite of high-throughput data (CAGE-seq, RNA-seq and Chip-seq) from various developmental stages of zebrafish and tetraodon, available at UCSC custom tracks. Sadly the servers are being relocated to another place and the tracks are not available at the moment. Should be online within a week.

Custom tracks information can be found in the paper: http://www.ncbi.nlm.nih.gov/pubmed/24002785 or at UCSC custom tracks.

cheers

[Anima Mundi]

That sounds pretty good, and a week is a reasonable time :).

Answer 2

[Chirag Nepal]

You can upload the Zebrafish (CAGE-seq, RNA-seq and H3K4me3) tracks from this link http://52128.bham.ac.uk:8000/tracks/zebrafish/Zebrafish_tracks.txt

Please refer to the paper for detailed information about the stages.

cheers

[Anima Mundi]

Ok, thanks again!