title: GSM2480902: ATAC_TET3_3; Mus musculus; ATAC-seq
library_construction_protocol: (RNA-Seq)Prior to RNA isolation cell lines carrying different Tet3 constructs were enriched for cells with TET3 expression by flow sorting for GFP fluorescence using a BD Influx High-speed Cell Sorter. RNA was isolated using Qiagen RNeasy Micro columns and treated with DNaseI (Ambion). (ChIP-Seq)Chromatin immunoprecipitation was performed as described in (Schmidt et al. 2009). ES cell lines expressing different TET3 isoforms  were cross-linked and harvested. 10 ug of a TET3 antibody developed with Millipore (ABE290) was used per precipitation, and cross-linked, sonicated nuclear material was used as input control. (ATAC-Seq)ATAC-seq was performed according to the original protocol (Buenrostro et al., 2015) with the following modifications. 10,000 cells were treated with 0.5μl Tn5 transposase in a total volume of 20 μl for 30 minutes at 37 degrees. (RNA-Seq)Indexed RNA-Seq libraries were constructed from 500 ng total RNA using theTruSeq Stranded Total RNA Library Prep Kit for Illumina with Ribo-Zero Gold. (ChIP-Seq)Sequencing libraries from precipitated DNA were prepared using the Diagenode MicroPlex Library Preparation Kit. (ATAC-Seq)Sequencing libraries were prepared according to the original protocol (Buenrostro et al., 2015).  A total of 15 PCR cycles  and two rounds of Ampure Bead clean-up were performed.
identifiers.namespace: GEO
identifiers.id: GSM2480902