alias: GSM3375550
title: GSM3375550: ChIPseq_IMR90_Input_OIS; Homo sapiens; ChIP-Seq
library_construction_protocol: In situ Hi-C was performed as previously described (Rao et al., 2014, Cell). ChIP-seq was performed as previously described (Aird et al., 2017 JCB).  RNA was extracted from IMR90 cells using RNeasy Mini kit (Qiagen).  RNA-seq was carried out as previously described with modifications (Tanizawa et al. 2017 NSMB). For in situ Hi-C, sequencing adapters were ligated using NEBNext Ultra Ligation module (New England Biolabs, Inc) on Dynabeads, and DNA was PCR-amplified for 8-14 cycles using NEBNext Q5 Hot Start HiFi PCR master Mix and NEBNext multiplex oligos (New England Biolabs, Inc). ChIP-seq was carried out as described previously (Iwasaki et al. 2015).  Approximately 1 ng ChIP DNA was subjected to the illumine library construction using NEBNext Ultra DNA library prep kit (New England Biolabs).  Adaptor-ligated DNA was PCR-amplified for 12 cycles using NEBNext Q5 Hot Start HiFi PCR master Mix and NEBNext multiplex oligos (New England Biolabs).  PCR products were sequenced on Illumina NextSeq 500 platform to obtain 76-bp single-end reads.  For RNA-seq, Poly (A) RNA was purified using NEBNext Poly (A) mRNA Magnetic Isolation Module (New England Biolabs), and sequence libraries were constructed using NEBNext mRNA Library prep Master mix for Illumina (New England Biolabs).  Adaptor-ligated DNAs were PCR-amplified for 12 cycles using NEBNext Q5 Hot Start HiFi PCR master Mix and NEBNext multiplex oligos (New England Biolabs).  PCR products were sequenced on Illumina NextSeq 500 platform to obtain 76-bp single-end reads.
identifiers.namespace: GEO
identifiers.id: GSM3375550