ena-DATASET-dkfz_b062-16-06-2020-11:58:23:351-469 - samples

This dataset contains DRIP-seq data from 2 patients.
DNA–RNA hybrids were extracted from tissue derived from ETMR
patient-derived xenograft (PDX) models (BT183) that were treated
using topotecan or saline as described previously27. Tumours were
subsequently frozen and pelleted using ultracentrifugation. DNA–RNA
hybrids were extracted as described previously using the same protocol
that is applied for cultured cells21. DNA was extracted using proteinase
K followed by phenol–chloroform extraction and ethanol precipitation.
Subsequently the DNA was fragmented using the restriction enzymes
HindIII, EcoRI, BsrGI, XbaI and SspI (New England Biolabs). Digested
DNA was subsequently incubated with the anti-DNA–RNA hybrid anti-
body S9.6 (Merck, MABE1095) and immunoprecipitated using agarose
beads. Bound DNA–RNA hybrids were eluted and incubated with pro-
teinase K and cleaned with an additional phenol–chloroform–ethanol
extraction. The DNA was subsequently sonicated and sequenced using
a Hiseq 2000 machine with a 50-bp single-read protocol. Each treat-
ment condition was performed in duplicate and both RNase H and the
input was included as negative controls resulting in 10 Fastq files.EGA dataset EGAD00001006219