GSM4759336: G. sulfurreducens - HFO; Geobacter sulfurreducens; OTHER
For DNA extraction samples, Fe (III) citrate and fumarate cultures were harvested directly by centrifugation (10,000 rpm, 1 min). Conversely, HFO cultures were first dissolved with oxalate. DNA was isolated with the TIANamp Bacteria DNA Kit (TIANGEN, Cat. No. DP302-02). Libraries of replicates of G. sulfurreducens were prepared for SMRT sequencing using a previously described library construction. These libraries were sequenced to a mean genome coverage depth of > 175×on the PacBioRS (Pacific Biosciences; Menlo Park, CA, USA) using standard protocols. Average read lengths were > 10 kbp and read quality was > 0.7 in all libraries (Supplementary Figure S1 B and C). Sequencing reads were processed and mapped to the reference sequences (RefSeq AE017180.2) using the software program BLASR. BLASR generates a Mapping QV representing the confidence that the read maps are unique to the selected genomic interval. Base modification and motif detection was performed using the modification and motif detection protocol in the software program SMRTPipe v.1.3.3. Positions with coverage of > 25× and kinetic scores of QV > 30 were considered modified as previous study has suggested.11 The QV is the −10 * log (P value), where the P value was determined from a t test between the sample and the in silico model (http://pacb.com/applications/base_modification/index.html). Positions with coverage of ≤ 25 × and QV ≤ 30 were excluded from analysis.
GEO Accession
GSM4759336