title: GSM3904416: RNAchIP-seq input, PMA-treated HP1g expressing cell line, replicate 2; Mus musculus; RIP-Seq
library_construction_protocol: A chromatin-enriched fraction (input) was obtained by a combination of Dnase-treatment and sonication of nuclei submitted to a low formaldehyde crosslinking procedure. RNAchIP samples (HP1g-IP) were obtained out of the solubilized chromatin fraction by immunoprecipitation of HP1g. Subsequent RNA extraction was performed by guanidinium thiocyanate-phenol-chloroform extraction (AGPC) followed by proteinase K and Dnase I treatment. RNA quality and yield were assessed by the RNA integrity number (RIN) algorithm, using the 2100 Bioanalyzer. Directional libraries were prepared using the Smarter Stranded Total RNA-Seq kit-Pico Input Mammalian kit following the manufacturer's instructions (Clontech, 635005). The quality of all libraries was verified with the DNA-1000 kit (Agilent) on a 2100 Bioanalyzer and quantification was performed with Quant-It assays on a Qubit 3.0 fluorometer (Invitrogen). Clusters were generated for the resulting libraries, with the Illumina HiSeq SR Cluster Kit v4 reagents. Sequencing was performed using the Illumina HiSeq 2500 system and HiSeq SBS kit v4 reagents. Runs were carried out over 65 cycles, including seven indexing cycles, to obtain 65-bp single-end reads. Sequencing data were then processed with the Illumina Pipeline software, Casava version 1.9
attributes.tag: GEO Accession
attributes.value: GSM3904416