de Lucas 2016, H3K27me3 and H3K4me3 profiles in root.


Genome binding/occupancy profiling by high throughput sequencing of vascular specific H3K27me3 and H3K4me3 histone modifications.



From A. thaliana (Feb 2011 TAIR10/araTha1).

ChIP-seq data:

Filename Description Feature GEO-ID
1 GSM2302417.sga Root|H3K27me3|GFP|rep1 H3K27me3 GSM2302417
2 GSM2302423.sga Root|H3K27me3|GFP|rep2 H3K27me3 GSM2302423
3 GSM2302415.sga Root|H3K27me3|WT|rep1 H3K27me3 GSM2302415
4 GSM2302421.sga Root|H3K27me3|WT|rep2 H3K27me3 GSM2302421
5 GSM2302418.sga Root|H3K4me3|GFP|rep1 H3K4me3 GSM2302418
6 GSM2302424.sga Root|H3K4me3|GFP|rep2 H3K4me3 GSM2302424
7 GSM2302416.sga Root|H3K4me3|WT|rep1 H3K4me3 GSM2302416
8 GSM2302422.sga Root|H3K4me3|WT|rep2 H3K4me3 GSM2302422
9 GSM2302414.sga Root|INPUT|GFP|rep1 INPUT GSM2302414
10 GSM2302420.sga Root|INPUT|GFP|rep2 INPUT GSM2302420
11 GSM2302413.sga Root|INPUT|WT|rep1 INPUT GSM2302413
12 GSM2302419.sga Root|INPUT|WT|rep2 INPUT GSM2302419

Technical Notes

FASTQ files were extracted from SRA files using fastq-dump (SRA toolkit v2.5.0) and mapped to the genome using Bowtie v0.12.8. SAM files were then converted into bam using samtools v0.1.14 and to bed using bamToBed v2.12.0 (bedtools). SGA conversion was carried out using (ChIP-Seq v. 1.5.2).


Last update: 1 Oct 2018