simoultaneous chromatin + transcriptional profiling

Question

[BioinfGuru]

Hi all,

Im not sure if this is the right forum for this question so apologies in advance. Id like to access data in which chromatin profiling (e.g. ChIP/DNA/ATAC-seq) and transcription (e.g. RNA-seq) has been simoultaneously captured (preferably, but not necessarily, in single cell). I've heard the BROAD are now doing this but I don't know the name of the assay.

The idea is that by capturing chromatin state and the transcripts at the same time in the same cells, that it allows the combination to determine the regulatory regions for each gene/transcript.

The analysis pipeline is something Id like to develop in house but I need to get the data first so any clues on the name or type of assay, or where to find such data would be much appreciated.

Regards

Kenneth

Answer 1

[Chirag Parsania]

HI,

I would suggest you to explore recent papers of chip and RNAseq. Definitely you will find some with both chip and RNAseq. You haven't mentioned which organism you are looking for. Here is the one from our lab for yeast candida albicans contains TF chip, H3 chip, polII chipseq and RNAseq. All data publicly available.

https://www.nature.com/articles/ncomms11704#s1

~Chirag.

[BioinfGuru]

Thank you Chirag - I also managed to find a very handy tool that seems appropriate here called BETA