title: GSM5233297: ChIP_Input; Mus musculus; ChIP-Seq
library_construction_protocol: Two 15cm-dishes with 2.10^7 cells in 20mL of culture media were used for each ChIP-seq experiment.  ChIP-seq was performed as described in ChIP-IT High sensitivity Kit from Active Motif with a few adaptations. Chromatin is sonicated by Bioruptor: 30sec ON – 30sec OFF, 10 cycles, high power. Sonicate for a total of 40 cycles for histones and of 30 cycles for TFs with 10min break on ice every 10 cycles. For ChIP reaction, 20µg chromatin was used with 4µg antibody for histone and 30µg chromatin + 4µg antibody for none-histone proteins. ChIP-DNA was eluted in 36µL with pre-warmed Elution Buffer then ChIP-DNA concentration was quantified with the Qubit dsDNA HS Assay Kit. 2,5ng to 10ng of ChIP-DNA were used for library preparation. 2,5ng to 10ng ChIP-DNA were used for library preparation. ChIP-seq library preparation was performed as described in TruSeq ChIP Sample Preparation kit from Illumina with few adaptations. The Enrich DNA Fragment step is proceeded before Purify Ligation Products step. AMPure XP beads were air-dry 7min. 1µL library was diluted 1:10 in H20 to quantified library concentration by Qubit DNA HS assay quantification. Agilent High Sensitivity DNA Electrophoresis was run to check DNA fragment size. Before sequencing, ChIP-seq libraries were quantified by qPCR. Libraries were sequenced 50bp or 100bp single-reads with 50 million reads of depth sequencing on HiSeq 2000 Illumina or NovaSeq 6000 Illumina machine at the MGX platforms.