HeLa cells were grown in suspension culture, HepG2 cells on plates in DMEM containing 10% FBS, 1% Penn/Strep and harvested at subconfluent concentration.
Extracted molecule
total RNA
Extraction protocol
RNA was extraceted with phenol, other column purified, TAP treated, adapters were addad by C-tailing, 5' ligation and RT using primer with a polyG stretch. PCR amplificaiton was used for enrichment and followed by gel purification of expected size range.
Library strategy
ncRNA-Seq
Library source
transcriptomic
Library selection
size fractionation
Instrument model
Illumina Genome Analyzer II
Description
HepG2_3pM_6 variable: nuclar other size range <50nt, 3pM cluster density
Data processing
Reads were aligned to the reference genome (hg18 assembly version), and the fragment count at any given position (25-bp resolution) was estimated as the number of uniquely aligned reads oriented towards it and within 300 bp. Enriched intervals were identified by comparison of the mean fragment count in 1-kb windows against a sample-specific expected distribution estimated by randomization (H3K4me3, H3K27me3), or using a supervised Hidden Markov Model (H3K36me3, H3K9me3, H4K20me3).
