Project description:MAGE-seq amplicon data from the paper RNA structural determinants of optimal codons revealed by MAGE-seq in Cell Systems 2016 by Kelsic, Chung, Cohen, Park, Wang & Kishony. Data contains read counts for PCR amplicons of the Escherichia coli gene infA: 1) Single codon mutants tiling along the entire gene, with timepoints from growth doublings in rich and minimal medias. 2) Codon pair mutants for positions at the beginning of the gene with timepoints for growth doublings in rich media. 3) Mutations in a hairpin of the 5' UTR for growth in rich media.
Project description:The dataset represents the proteome analysis of six sampling dates during the phytoplankton bloom at the island of Helgoland in the North Sea at the long term research station ‘Kabeltonne’ (54° 11' 17.88'' N, 7° 54' 0'' E) in 2016.
Project description:Contaminated aquifer (Dusseldorf-Flinger, Germany) templates extracted from 5 sediment depths ranging between 6.4 and 8.4 m below ground and over 3 years of sampling were amplified for amplicon pyrosequencing using the primers Ba27f (5’-aga gtt tga tcm tgg ctc ag-3’) and Ba519r (5’- tat tac cgc ggc kgc tg-3’), extended as amplicon fusion primers with respective primer A or B adapters, key sequence and multiplex identifiers (MID) as recommended by 454/Roche. Amplicons were purified and pooled as specified by the manufacturer. Emulsion PCR (emPCR), purification of DNA-enriched beads and sequencing run were performed following protocols and using a 2nd generation pyrosequencer (454 GS FLX Titanium, Roche) as recommended by the developer. Quality filtering of the pyrosequencing reads was performed using the automatic amplicon pipeline of the GS Run Processor (Roche), with a slight modification concerning the valley filter (vfScanAllFlows false instead of TiOnly) to extract the sequences. Demultiplexed raw reads were furhter trimmed for quality and lenght (>250 bp).
Project description:Genotyping of RpoD mutants via amplicon sequencing from the following manuscript: \\"Systematic dissection of σ70 sequence diversity and function in bacteria\\" by Park and Wang (2020). Includes raw sequencing reads from samples from MAGE-seq single codon saturation mutagenesis and high-throughput fitness competition experiment as well as the RpoD ortholog mutants generated through recombineering and CRISPR selection.