Tiana 2018, HIF binding sites in HUVEC cells exposed to hypoxia.

Genome-wide maps of components of HIF alpha (HIF1A and EPAS1) and HIF beta (ARNT) in HUVE cells exposed to hypoxia.

• Raw data was downloaded from: GEO
• Input file format: SRA
• Download date: 5-2-2018

From H. sapiens (Feb 2009 GRCh37/hg19).

ChIP-seq data:

	Filename	Description	Feature	GEO-ID
1	GSM2390643.sga	HUVEC|ARNT||	ARNT	GSM2390643
2	GSM2390642.sga	HUVEC|EPAS1||	EPAS1	GSM2390642
3	GSM2390641.sga	HUVEC|HIF1A||	HIF1A	GSM2390641
4	GSM2390640.sga	HUVEC|none||	none	GSM2390640

FASTQ files were extracted from SRA files using fastq-dump (SRA toolkit v2.5.0) and mapped to the genome using Bowtie2 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. 1.5.3).

• Tiana M, Acosta-Iborra B, Puente-Santamaría L, Hernansanz-Agustin P, Worsley-Hunt R, Masson N, García-Rio F, Mole D, Ratcliffe P, Wasserman WW, Jimenez B, Del Peso L
  The SIN3A histone deacetylase complex is required for a complete transcriptional response to hypoxia. Nucleic Acids Res. 2018 Jan 9;46(1):120-133. doi: 10.1093/nar/gkx951. 29059365
• GEO series GSE89836: Genome-wide mapping of HIF binding sites by ChIP-seq in HUVEC cells exposed to hypoxia

Delete this section if none