alias: GSM4663482
title: GSM4663482: Glioma stem cells + CHI3L1 rep1; Homo sapiens; ATAC-seq
library_construction_protocol: ATAC-seq libraries were prepared according to the protocol established and optimized before (Ackermann et al., 2016; Buenrostro et al., 2013). Specifically, collected cell samples with low viability (<85%) were first treated with 200 U/ml DNase (Worthington) for 30 minutes at 37°C for 30 minutes, followed immediately by thorough washing to remove residual DNase. Cell lysis was performed using 50 ul of cold lysis buffer composed of resuspension buffer, 0.1% NP-40, 0.1% Tween-20, and 0.01% Digitonin (Promega), and transposition of the resulting nuclei pellet from the lysate by Tn5 transposase was accomplished using the Nextera DNA Library Prep Kit (Illumina). DNA isolation from the transposition reaction was done using MinElute Reaction Cleanup Kit (Qiagen), and the library was generated from the isolated DNA through PCR amplification protocol. Purification of the library for optimal library preparation included removal of primer dimers and DNA fragments larger than 1000 base pairs (bp) through double-sided bead purification with Agencourt AMPure XP beads (Beckman Coulter). Sequencing of the final library was performed by GENEWIZ using the Illumina HiSeq 2500 system to ideally identify and record 150 bp paired-end fragment read occurrences in the resulting FASTQ file for each technical replicate.
identifiers.namespace: GEO
identifiers.id: GSM4663482