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.

• Raw data was downloaded from: SRA
• Input file format: SRA
• Download date: 21-1-2019

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

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

• Li A, Figueroa S, Jiang TX, Wu P, Widelitz R, Nie Q, Chuong CM
  Diverse feather shape evolution enabled by coupling anisotropic signalling modules with self-organizing branching programme. Nat Commun. 2017 Jan 20;8:ncomms14139. doi: 10.1038/ncomms14139. 28106042