title: Deep sequencing of small chromatin-associated RNA: isolation and library preparation.
abstract: Chromatin-associated RNA (caRNA) is a newly identified class of RNA molecules stably associated with chromatin, maintaining the higher order structure of euchromatic regions in an accessible form (Schubert et al., Mol Cell, doi:10.1016/j.molcel.2012.08.021, 2012). This section provides a detailed protocol describing the isolation of small caRNA from Drosophila cells and preparation of libraries suited for stranded small (20-200 bp) RNA deep sequencing on the Illumina platform.
authors.affiliation: Biochemistry Centre, Universität Regensburg, Regensburg, Germany.
authors.forename: Sarah Daniela
authors.initials: SD
authors.lastname: Diermeier
authors.forename: Thomas
authors.initials: T
authors.lastname: Schubert
authors.forename: Gernot
authors.initials: G
authors.lastname: Längst
mesh_terms: D000818:Animals; D002843:Chromatin / Q000378:metabolism*; D004331:Drosophila melanogaster / Q000378:metabolism; D015723:Gene Library; D059014:High-Throughput Nucleotide Sequencing / Q000379:methods*; D012342:RNA, Small Nuclear / Q000235:genetics* / Q000302:isolation & purification*; D017423:Sequence Analysis, RNA / Q000379:methods*
chemical_list: D002843:Chromatin; D012342:RNA, Small Nuclear