GSM4998173: ChIPseq_293T-WT_ELL_IP_Rep1_R1; Homo sapiens; ChIP-Seq
For ELL ChIP-seq, cross-link of the cells was performed using 1% formaldehyde for 7 min. The cross-linked chromatin was sonicated to generate fragments of 150-500 bp prior to immunoprecipitation. Immunoprecipitation of protein-DNA complex was performed using anti-ELL antibody (14468; Cell Signaling Technology) and Dynabeads M280 Sheep Anti-Rabbit IgG (11203D; Invitrogen). The immunoprecipitated DNA was purified using the QIAquick PCR purification kit (28106; Qiagen). Libraries for ChIP-seq and antibody-based in situ biotinylation-seq were prepared using TruSeq ChIP Library Prep Kit (Illumina) and IDT for illumina-TruSeq RNA UD Index (Illumina). Library purification and size selection were performed using Agencourt AMPure XP system. Libraries were checked for quality and quantity using Bioanalyzer. Equimolar concentrations of libraries were pooled, and sequenced as paired-end reads on the Illumina Novaseq 6000 platform (ChIP-seq) or Hiseq 2500 platform (antibody-based in situ biotinylation-seq). PRO-seq libraries were generated essentially as described in Mahat et al., 2016 (Nat Protoc, 11:1455-76; doi: 10.1038/nprot.2016.086). Primers RPI1, RPI2, RPI3 and RPI4 were used to barcode cDNAs from 293T-WT_Rep1 (Wild type, replicate 1), 293T-WT_Rep2 (Wild type, replicate 2), 293T-EAF1mut_Rep1 (Mutant EAF1, replicate 1), and 293T-EAF1mut_Rep2 (Mutant EAF1, replicate 2), respectively.