title: GSM1887739: second RNAseq sample from parental strain; Schizosaccharomyces pombe; RNA-Seq
library_construction_protocol: none provided by submitter For the RNASeq experiments, total RNA was extracted from three separate cultures of wt and mmi1Δ grown to mid-log phase and DNase-treated. Ribodepletion and library preparation were performed by the High-Throughput Genomics Group at the Wellcome Trust Centre for Human Genetics according to the TruSeq protocol. Note that with the TruSeq protocol the cDNA strand is sequenced. Thus all the strand information needs to be reversed after mapping the reads to the genome (i.e - to + and + to -). Paired-end CRAC libraries were generated essentailly as described by Granneman et al PNAS 2009. A paired-end compatible 3' adapter was used for making the CRAC library (5’App-NAGATCGGAAGAGCACACGTCTG-ddC 3’). The N in the sequence indicates a random nucleotide. PCR oligonucleotides for making CRAC libraries 3' adapter: App_PE 5’App-NAGATCGGAAGAGCACACGTCTG-ddC 3’ 5' adapters: L5Aa 5'-invddT-ACACrGrArCrGrCrUrCrUrUrCrCrGrArUrCrUrNrNrNrUrArArGrCrN-OH-3' L5Ab 5'-invddT-ACACrGrArCrGrCrUrCrUrUrCrCrGrArUrCrUrNrNrNrArUrUrArGrCrN-OH-3' L5Ad 5'-invddT-ACACrGrArCrGrCrUrCrUrUrCrCrGrArUrCrUrNrNrNrCrGrCrUrUrArGrCrN-OH-3' L5Bb 5'-invddT-ACACrGrArCrGrCrUrCrUrUrCrCrGrArUrCrUrNrNrNrCrArCrUrArGrCrN-OH-3' P5_forward 5’-AATGATACGGCGACCACCGAGATCTACACTCTTTCCCTACACGACGCTCTTCCGATCT-3’ P3_reverse 5’-CAAGCAGAAGACGGCATACGAGAT(6nt barcode)GTGACTGGAGTTCAGACGTGTGCTCTTCCGATCT-3’
attributes.tag: GEO Accession
attributes.value: GSM1887739