title: GSM3937419: Fibroblast-3; Homo sapiens; RNA-Seq
library_construction_protocol: For Hi-C, nuclei were extraced after fixing using a cell lysis buffer. For ChIP-seq, nuclei were extracted and chromatins were fragmented by sonication. The TF/histone-DNA complexes were isolated by antibody.     Total RNA was isolated from samples by RNeasy Mini Kit (Qiagen) according to the manufacturer?s instructions. For eHi-C, briefly, the cells and tissues were first fixed with 1% formaldehyde and then quenched with 150mM glycine. The fixed samples were lysed using a cell lysis buffer or a tissue specific buffer. And nuclei were isolated and then digested with HindIII. After that, in situ proximity ligation was done by  ligating the digested chromatin in a large volume. Ligation products were then reverse-linked with proteinase K and purified using phenol-chloroform. The purified DNA was then digested with DpnII and then self ligated using T4 DNA ligase. After purification, the DNA products were then re-linearized with HindIII followed by DNA purification. The resulting DNA were used for library construction. First, the DNA were end-repaired using End-it kit (Epicentre). Second, the end repaired DNA was A-tailed by Klenow fragment (3??5? exo?; NEB). Then, a customized Illumina truseq Adapter was ligated and the resulting DNA was then PCR amplified. The final libraries were quantified and sequenced on Illumina Hiseq platform. All Hi-C libraries were constructed following illumina insctructions accompanying Truseq sample preparation kit.  Random indexes were introduced for eHi-C libraries to remove PCR duplication. Generally, PCR amplification was done with 7-9 cycles. All ChIP-seq libraries were generated following a ChIPmentation protocol with Nextera adapters.
attributes.tag: GEO Accession
attributes.value: GSM3937419