Dataset: OC1703A Sediment MG-MT
Deployment: OC1703A

Sediment was collected with an MC-800 multicorer aborad the R/V Oceanus (expedition 1703A) approximately 0-300 km off the coast of San Francisco, CA, USA. Cores were stored at 4C until extrusion and sectioning within 24h of collection. Cores were sectioned into 2.5-5cm vertical horizons, and approximately 2g of sediment were sampled from each horizon with a cut-off syringe, flash frozen in liquid nitrogen, and stored at -80C until extraction of nucleic acids. DNA was extracted with an RNeasy PowerSoil DNA elution kit (Qiagen, cat. no 12867-25) in combination with an RNeasy PowerSoil Total RNA kit (Qiagen, cat. no 12866-25). The manufacturer's protocol was modified to include a bead-beating step of 5.5 m/s for 2x45s with a FastPrep-24 instrument. DNA and RNA were eluted in 100 microliters of DNAse and RNAse-free water or 1xTE and stored at -80C. Total RNA was treated with DNAse (Thermo Fisher Scientific,cat. no AM1907). Three DNA samples were additionally processed for long-read sequencing by size-selection with the BluePippin instrument targeting the size range of 10-50kb and a library was prepared for sequencing with the 10x Genomics Chromium system according to manufacturer's protocol and described in Bishara et al. (2018, https://doi.org/10.1038/nbt.4266). Chromium libraries were sequenced with 2 x 151bp sequencing on an HiSeq 4000 instrument (Illumina). All other samples were processed by the Joint Genome Institute (Department of Energy). DNA was sheared to approximately 300bp using a Covaris LE220 ultrasonicator and size selected with SPRI beads and libraries prepared and barcoded using Kapa Biosystems library preparation kit. Total RNA was treated with Ribo-Zero rRNA removal kit (Illumina) and cDNA libraries generated using the Illumina Truseq Stranded mRNA Library Prep kit. The rRNA depleted RNA was fragmented and reversed transcribed using random hexamers and SSII (Invitrogen) followed by second strand synthesis. The fragmented cDNA was treated with end-pair, A-tailing, adapter ligation, and 10 cycles of PCR. DNA and cDNA were sequenced with 2 x 151bp sequencing on a Nova Seq S4 (Illumina) instrument.