7 protocols
AccessionNameType
P-MTAB-35217
high throughput sequence alignment protocol
Reads were aligned to the reference human genome (hg19) using Bowtie or TopHat, where appropriate.
P-MTAB-35218
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.
P-MTAB-35216
nucleic acid sequencing protocol
Illumina GAIIx or HiSeq 2000, single-end reads 36 or 50bp in length.
P-MTAB-35213
nucleic acid extraction protocol
FAIRE was performed as described in Simon et al 2012, Nature Protocols. RNA-seq was performed on riboMinus-extracted RNA.
P-MTAB-35215
nucleic acid sequencing protocol
Illumina GAIIx or HiSeq 2000, single-end reads 36 or 50bp in length.
P-MTAB-35214
nucleic acid library construction protocol
Libraries were prepared using manufacturer's recommendations with TruSeq adapters or Illumina adapters.
P-MTAB-35212
growth protocol
Tumors and normal kidney stored at -80C.