7 protocols
AccessionType
high throughput sequence alignment protocol
Reads were aligned to the reference human genome (hg19) using Bowtie or TopHat, where appropriate.
normalization data transformation protocol
For FAIRE-seq data, the number of aligned reads at each nucleotide in the genome was summarized into a bigWig signal track. For ChIP-seq experiments, regions of significant enrichment relative to input control were identified using ZINBA; broader domains were defined by merging two or more significant regions within 5kb using Galaxy.
nucleic acid sequencing protocol
Illumina GAIIx or HiSeq 2000, single-end reads 36 or 50bp in length.
nucleic acid extraction protocol
FAIRE was performed as described in Simon et al 2012, Nature Protocols. RNA-seq was performed on riboMinus-extracted RNA.
nucleic acid sequencing protocol
Illumina GAIIx or HiSeq 2000, single-end reads 36 or 50bp in length.
nucleic acid library construction protocol
Libraries were prepared using manufacturer's recommendations with TruSeq adapters or Illumina adapters.
growth protocol
Tumors and normal kidney stored at -80C.