alias: GSM2050612
title: GSM2050612: 0.41 nM Fe'_rplB; Synechococcus sp. PCC 7002; RNA-Seq
library_construction_protocol: Cells for RNA extraction were harvested in mid-exponential growth phase by filtration through 0.4 mm polycarbonate membrane and cemtrifugated at 6000 × g for 8 min at 4 ºC. The pellets were snap frozen in liquid nitrogen. RNA was isolated using TRI Reagent (Sigma-Aldrich, Buch, Switzerland) following provider’s instructions. Ribosomal RNA (rRNA) was depleted using Ribo-Zero™ rRNA Removal Kit using gram-negative bacteria-specific capture oligonucleotides (Epicentre, Madison, WI, USA). RNA purity and integrity was determined using the Bioanalyzer RNA 6000 Nano Kit (Agilent Technologies, Inc., Santa Clara, CA, USA). Libraries were prepared using 200 ng of RNA with the Illumina TruSeq Stranded mRNA kit and sequenced generating 100 bp single reads on an Illumina HiSeq 2500 System (Illumina, San Diego, CA, USA). Quality control was performed using FastQC tool (Babraham Bioinformatics, UK). Reads were aligned to the genome of Synechococcus sp. PCC7002 build from the Cyanobase (Fujisawa et al., 2013) and further analyzed using TopHat 2.0 mapper software (Trapnell et al., 2009). Table of counts were obtained using the HTSeq 0.5.3.p9 (Anders et al., 2015). Reads mapped to the reference genome at 88.7 ±6.9 %.
identifiers.namespace: GEO
identifiers.id: GSM2050612