Public Data and Tools

Here, you will find links to short read data from our publications, as well as analytical tools we have developed – helping you find the right tree in a forest of information.

Gymnosperm transcriptomes

Assembled transcriptomes from Huang Y et al, 2015: Pinus canariensis: GBLJ00000000

Ephedra trifurca: GBKT00000000

Cycas revoluta: GBJU00000000

Brassica rapa epigenomes

Data from Grover JW et al, 2018:

sRNA-seq from RdDM mutant leaves and ovules: SRP114437

sRNA-seq from intraspecific seeds: SRP114469

RNA-seq from brnrpd1 mutant ovules and seeds: SRP132223

Data from Grover JW et al, 2020: PRJNA588293

RNA-seq and sRNA-seq from dissected seed tissues of intraspecific crosses
Bisulfite-seq of RdDM mutant leaves and ovules
sRNA and RNAseq from various seed stages

Data from Chakraborty T et al, 2021:

Bisulfite-seq data from mature embryos of wild type and RdDM mutants: PRJNA657007

Data from Burgess et al, 2022:

RNA-seq from rdr2 and nrpe1 ovules and young seeds: PRJNA808098

Rice sRNAs

sRNA-seq data from wild type and nrpd2-deficient leaves from Chakraborty T et al, 2022: PRJNA758109

Snakemake workflows

sRNA-seq processing and mapping workflow by Maya Bose: doi.org/10.5281/zenodo.3539531

Whole genome bisulfite seq workflow by Jeff Grover: doi.org/10.5281/zenodo.3539516