Antigen

Antigen Class

Histone

Antigen

H3K27me3

Cell type

Cell type Class

Breast

Cell type

Breast cells

NA

NA

Sample

source_name

Cultured fibroblasts

tissue

normal breast

chip antibody

07-449 from Millipore

strain

BF

Sequenced DNA Library

library_strategy

ChIP-Seq

library_source

GENOMIC

library_selection

ChIP

library_construction_protocol

Chip-Seq: DNA samples were end repaired, poly-A tailed and Illumina single end adapters were ligated following the standard Illumina protocol with minor adjustments. Agencourt AMPure XP beads at 0.8x ratio were used to size select out adapter dimers after adapter ligation. The Illumina kit Phusion enzyme was replaced by Kapa HiFi HotStart ready mix. Post PCR, AMPure XP beads were used at a 1:1 ratio to maintain size integrity and to allow use of the Invitrogen SizeSelect E-gel system. Samples were finally purified with QAIquick gel extraction kit and quality controlled on the DNA 1000 BioAnalyser 2100 chip before clustering and subsequent 36bp single end sequencing on the GAIIx analyser. RNA-Seq: Total RNA was extracted using the High Pure RNA extraction Kit (Roche). RNA samples were quality controlled (QC) using the 6000 Nano RNA Chip on the BioAnalyser 2100 (Agilent) and subjected to poly-A selection using Sera-Mag oligo dT beads (Thermo Fisher Scientific Inc.). Libraries were prepared using the Directional mRNA-Seq Library Prep. v1.0. Pre-Release Protocol from Illumina with minor adjustments. The Illumina kit Phusion enzyme was replaced by Kapa HiFi HotStart ready mix which reduced the overall volume of the PCR and the ratio for the Agencourt AMPure XP beads was adjusted accordingly. The standard PCR cycling was also changed to match the concentration of the total RNA from the initial QC. After passing the final QC, the libraries were subjected to cluster formation and then 72bp single end sequencing on the GAIIx analyser.

Sequencing Platform

instrument_model

Illumina Genome Analyzer IIx

hg38

Number of total reads

31704076

Reads aligned (%)

91.3

Duplicates removed (%)

3.6

Number of peaks

159 (qval < 1E-05)

hg19

Number of total reads

31704076

Reads aligned (%)

90.9

Duplicates removed (%)

4.2

Number of peaks

201 (qval < 1E-05)