Are the ENCODE raw fastq files and genotyping data available for each cell line?

Question

[Milos Pjanic]

I would like to check allele specific mapping of reads from the ENCODE ChIP-Seq data to a specific enhancer SNP in lines that are heterozygotes. Are the imputed genotypes available for ENCODE cell lines? Or alternatively raw fastq files from the ENCODE ChIP-Seq, as I could use ChIP-Seq fastqs to call variants.

Answer 1

[Khader Shameer]

Yes - detailed lists are here and here.

• FASTQ is available from SRA
• Genotyping data from GEO