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.

• Raw data was downloaded from: GEO
• Input file format: SRA
• Download date: 21-11-2016

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

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 bed2sga.pl (ChIP-Seq v. 1.5.2).

• de Lucas M, Pu L, Turco G, Gaudinier A, Morao AK, Harashima H, Kim D, Ron M, Sugimoto K, Roudier F, Brady SM
  Transcriptional Regulation of Arabidopsis Polycomb Repressive Complex 2 Coordinates Cell-Type Proliferation and Differentiation. Plant Cell. 2016 Oct;28(10):2616-2631. Epub 2016 Sep 20. 27650334
• GEO series GSE86429: Vascular specific H3K27me3 and H3K4me3 profile in the Arabidopsis root