Li 2017, H3K4me3 ChIP-seq in the narrower and wider vanes of primary remiges.


ChIP-seq against H3K4me3 in the medial and lateral mesenchyme (pulp) of chicken primary remiges.



From G. gallus (Dec 2015 Gallus_gallus-5.0/galGal5).

ChIP-seq data:

Filename Description Feature GEO-ID
1 GSE86414_H3K4me3_all.sga primary remiges|H3K4me3|all samples H3K4me3 GSE86414_H3K4me3_all
2 GSE86414_input_all.sga primary remiges|input|all samples input GSE86414_input_all
3 GSM2301938.sga primary remiges|H3K4me3|lateral pulp|batch1 H3K4me3 GSM2301938
4 GSM2301939.sga primary remiges|H3K4me3|medial pulp|batch1 H3K4me3 GSM2301939
5 GSM2301940.sga primary remiges|input|lateral pulp|batch1 input GSM2301940
6 GSM2301941.sga primary remiges|input|medial pulp|batch1 input GSM2301941
7 GSM2301942.sga primary remiges|H3K4me3|lateral pulp|batch2 H3K4me3 GSM2301942
8 GSM2301943.sga primary remiges|H3K4me3|medial pulp|batch2 H3K4me3 GSM2301943
9 GSM2301944.sga primary remiges|input|lateral pulp|batch2 input GSM2301944
10 GSM2301945.sga primary remiges|input|medial pulp|batch2 input GSM2301945

Technical Notes

FASTQ files were extracted from SRA files using fastq-dump (SRA toolkit v2.5.0) and mapped to the genome using Bowtie v1.1.1. SAM files were then converted to BAM using samtools v0.1.14 and to BED using bamToBed v2.27.0 (bedtools). BED to SGA conversion was carried out using the following command:
awk -v ft=$FEATURE 'BEGIN {FS=OFS="\t"} $6 == "+" {print $1, ft, $2+1, "+", "1"} $6 == "-" {print $1, ft, $3, "-", "1"}' $SAMPLE.bed | sort -k1,1 -k3,3n -k4,4 | compactsga > $SAMPLE.sga


Last update: 26 Feb 2019