The ChIP-seq datasets for H3K4me1, H3K4me2, H3K4me3, H3K27me3, H3K9me3
and H3K36me3 in neural progenitors were retrieved from the GEO
repository with accession numbers
GSE12241 and GSE11172.
These datasets were processed with SICER in the way as described below
using as input the whole cell extract sample provided in
GSE12241.
The ChIP-seq dataset for H3K27ac was retrieved from ArrayExpress with
accession E-MTAB-1423
and it was paired with the input chromatin sample from the same accession.
Methods
The raw reads were mapped to the mouse genome (mm9 including random
chromosomes) with Bowtie version 0.12.5.
We used then SICER version 1.1 with parameters redundancy threshold=1,
window size=1000, fragment size=180, effective genome fraction=0.77, gap size=100 and FDR=0.01.
The resulting "islandfiltered-normalized.wig" files were converted to
bigWig using the wigToBigWig utility from the UCSC Genome Browser.
Credits
Data were generated and processed for the CISSTEM project. For inquiries, please contact Juan L. Mateo at the following address: mateojuan (at) uniovi.es