Illumina HiSeq 1500 sequencing; RIP-seq analysis of Isw1 interacting transcripts
RIP-seq analysis of Isw1 interacting transcripts
Isw1-PrA expressing cells were grown overnight at 25°C and shifted for 3 hours at 30°C. RNA immunoprecipitations were performed from 2g of frozen cell grindates prepared as previously described (Oeffinger et al., 2007). Immunoprecipitated RNA was isolated from proteins by treating samples with 40 μg Proteinase K (Roche) and 0,1% SDS for 30 min at 30 °C. RNA was extracted with the Nucleospin RNA II Kit (Macherey-Nagel),  Libraries were prepared using the strand specific RNA-Seq library preparation TruSeq Stranded mRNA kit (Illumina). Libraries were multiplexed by 9 on 2 flowcell lanes. A 50 bp read sequencing was performed on a HiSeq 1500 device (Illumina). A mean of  22.9 ± 2.6 million passing Illumina quality filter reads was obtained for each of the 18 samples. Library preparation and Illumina sequencing were performed at the Ecole Normale Supérieure Genomic Platform (Paris, France).
INSERM
E-MTAB-4826:Sample 16_s
Experimental Factor: wild type genotype
strain