Journal: PLoS ONE

Article Title: Protection of the C . elegans germ cell genome depends on diverse DNA repair pathways during normal proliferation

doi: 10.1371/journal.pone.0250291

Figure Lengend Snippet: A. L4 larvae (F1 generation) from a parental founder strain (P0) were individually picked onto NGM plates and allowed to self-fertilize prior to picking individual L4 larvae of the next generation (F2) from each F1 plate. This process was repeated until clonal lines reached generation F20 or F40. Clonal lines were then allowed to expand, harvested, and prepared for whole genome sequencing (Materials and Methods). B. Mutation types and their location on the 6 C . elegans chromosomes (I-V and X) across all wild-type samples and mutation classes. The height of the white bars corresponds to the length of the respective C . elegans chromosome. Single nucleotide variants are indicated by a dot, dinucleotide variants (DNVs) by a square, indels divided in deletions (D) and insertions (I) by a triangle, and structural variants (SVs) by a line. C. Average number of heterozygous mutations in the N2 wild-type genome per generation across all mutation classes and types. Single nucleotide variants are shown in the context of their 5’ and 3’ base. Grey bars denote 95% credible intervals for the number of mutations in each type. “Complex indels” class denotes deletions with insertions. Data for N2 was previously shown in ( Fig 1C) . Information related to the 528 whole genome sequencing WGS primary-source datasets (56 deposited in this study, 472 deposited in (Suppl Data 1 and Supple Note 1 of can be found in ).

Article Snippet: In summary, DNA sequencing was performed using Illumina HiSeq 2000 and 10X Genomics short reads sequencing platforms at 100 bp paired-end, with a mean coverage of 50x.

Techniques: Sequencing, Mutagenesis

Journal: PLoS ONE

Article Title: Protection of the C . elegans germ cell genome depends on diverse DNA repair pathways during normal proliferation

doi: 10.1371/journal.pone.0250291

Figure Lengend Snippet: Mutation rates are shown as number of heterozygous mutations per generation for N2 wild-type (WT), and mutants used in this study grouped by the major DNA repair pathway they contribute to; direct damage reversal (DR), base excision repair (BER), nucleotide excision repair (NER), DNA double-strand break repair (DSBR), translesion synthesis (TLS), crosslink repair (ICLR), spindle assembly checkpoint (SAC), apoptosis, and mismatch repair (MMR). Base substitutions are shown in red (top), indels in green (center) and structural variants in blue (bottom). Dotted lines denote the mutation rates for wild-type. Error bars show the 95% confidence intervals; large dots represent variants with 2-fold increased or decreased mutation rates over N2 wild-type which are statistically significant with a false discovery rate (FDR) below 5%. All CIs which extend below the lower edge of the plot have zero as their lower border. Information related to the 528 whole genome sequencing WGS primary-source datasets (56 deposited in this study, 472 deposited in (Suppl Data 1 and Supple Note 1 of can be found in ).

Article Snippet: In summary, DNA sequencing was performed using Illumina HiSeq 2000 and 10X Genomics short reads sequencing platforms at 100 bp paired-end, with a mean coverage of 50x.

Techniques: Mutagenesis, Translesion Synthesis, Sequencing

Journal: PLoS ONE

Article Title: Protection of the C . elegans germ cell genome depends on diverse DNA repair pathways during normal proliferation

doi: 10.1371/journal.pone.0250291

Figure Lengend Snippet: A. Mutational signatures of BER, NER, and DR mutants that display statistically significantly different mutation spectra than wild-type shown as the number of mutations per generation across all mutation classes. Underscores (bold coloured bars) below each mutation profile indicate mutation types where the total mutation numbers are different from wild-type, three stars indicate genotypes with significantly different rates of substitutions, indels or SVs compared to those in wild-type (FDR < 5%). Single nucleotide variants are shown in the context of their 5’ and 3’ base context. B. Number of mutations of all classes shown for each individual sequenced line of the indicated genotype and generation. The four sequenced wild-type P0 lines reflect the variance present in initial generations. Mutations are shown cumulatively with mutations present in generation F20 included in F40. C. Mutation types of all classes and their location on the 6 C . elegans chromosomes (I-V and X) observed across agt-2 mutant lines. The height of the white bars corresponds to the length of each individual chromosome. Single nucleotide variants (SNVs) are indicated by a dot, dinucleotide variants (DNVs) by a square, indels divided in deletions (D), insertions (I), and deletions with insertions (DI) by a triangle, and structural variants (SVs) by a line. Clustered mutations that are present within a single agt-2 line are depicted by enlarged bold symbols. An analysis of brca-1 , him-6 and smc-6 swas previously shown in . Information related to the 528 whole genome sequencing WGS primary-source datasets (56 deposited in this study, 472 deposited in (Suppl Data 1 and Supple Note 1 of can be found in ).

Article Snippet: In summary, DNA sequencing was performed using Illumina HiSeq 2000 and 10X Genomics short reads sequencing platforms at 100 bp paired-end, with a mean coverage of 50x.

Techniques: Mutagenesis, Sequencing

Journal: PLoS ONE

Article Title: Protection of the C . elegans germ cell genome depends on diverse DNA repair pathways during normal proliferation

doi: 10.1371/journal.pone.0250291

Figure Lengend Snippet: A. Mutational signatures of DSBR mutants that exhibited statistically significant different mutation rates to wild-type displayed in numbers of mutations per generation. Bold coloured bars denote individual mutation classes where the number of mutations is different from wild-type, an underscore below each mutation profile indicates mutation types with total mutation numbers different from wild-type, and three stars indicate genotypes which have rates of substitutions, indels or SVs significantly different compared to wild-type (FDR < 5%). B. Estimated composition of structural variants per generation as estimated for wild-type and DNA repair mutants with elevated SV rates. C. Size distributions of tandem duplications (top, pink) and deletions (bottom, green) across wild-type and mutants with elevated SV rates. D. Clustering of mutations in DNA repair deficient mutants. Grey dots reflect the average proportions of clustered mutations. Error bars denote 95% confidence intervals. Mutants with a significantly different propensity for mutation clustering from wild-type (dotted black line) are shown and highlighted in red. ‘Information related to the 528 whole genome sequencing WGS primary-source datasets (56 deposited in this study, 472 deposited in (Suppl Data 1 and Supple Note 1 of can be found in ).

Article Snippet: In summary, DNA sequencing was performed using Illumina HiSeq 2000 and 10X Genomics short reads sequencing platforms at 100 bp paired-end, with a mean coverage of 50x.

Techniques: Mutagenesis, Sequencing

Journal: PLoS ONE

Article Title: Protection of the C . elegans germ cell genome depends on diverse DNA repair pathways during normal proliferation

doi: 10.1371/journal.pone.0250291

Figure Lengend Snippet: A. Mutational signatures of TLS and ICLR mutants that exhibited statistically significant differences to wild-type mutation rates displayed in numbers of mutations per generation. Same layout as . B . Proportion of indels (brown) and SVs (black) in G-rich regions in wild-type and across genotypes with elevated rates of SVs. Dotted line represents the proportion of variants falling into these regions as expected by chance. C . Tandem duplications (TDs) in helq-1 mutants. An analysis of rev-3 was previously shown in . Information related to the 528 whole genome sequencing WGS primary-source datasets (56 deposited in this study, 472 deposited in (Suppl Data 1 and Supple Note 1 of can be found in ).

Article Snippet: In summary, DNA sequencing was performed using Illumina HiSeq 2000 and 10X Genomics short reads sequencing platforms at 100 bp paired-end, with a mean coverage of 50x.

Techniques: Mutagenesis, Sequencing

Journal: PLoS ONE

Article Title: Protection of the C . elegans germ cell genome depends on diverse DNA repair pathways during normal proliferation

doi: 10.1371/journal.pone.0250291

Figure Lengend Snippet: A. Mutational signatures of mutants that exhibited statistically significant differences to wild-type mutation rates. The chromosomes on which respective genes are located are indicated in superscript following each mutant name. Layout as . B. Proportion of SVs with breakpoints into subtelomeric regions across wild-type and mutants that exhibit elevated SV rates. Dotted lines represent the fraction of variants expected to occur in subtelomeric regions by chance. C . Examples of subtelomeric structural variants in atm-1 mutants. D. Quantification of mutation burden in indicated DNA repair mutants for initial generations and F20 and F40 generations as shown. Information related to the 528 whole genome sequencing WGS primary-source datasets (56 deposited in this study, 472 deposited in (Suppl Data 1 and Supple Note 1 of can be found in ).

Article Snippet: In summary, DNA sequencing was performed using Illumina HiSeq 2000 and 10X Genomics short reads sequencing platforms at 100 bp paired-end, with a mean coverage of 50x.

Techniques: Mutagenesis, Sequencing

Journal: Briefings in Bioinformatics

Article Title: Current challenges and best-practice protocols for microbiome analysis

doi: 10.1093/bib/bbz155

Figure Lengend Snippet: An illustration of targeted amplicon and metagenomic sequencing approaches. A schematic overview demonstrating diverse sample types along with commonly utilized sequencing platforms, as well as systematic and stepwise data processing steps.

Article Snippet: At present, both Pacific Biosciences single-molecule real-time (SMRT) and Oxford Nanopore Technologies sequencing platforms are preferred due to their longer read sizes of 15–100 and ~1000 kilobases, respectively [ , ].

Techniques: Amplification, Sequencing

Journal: Briefings in Bioinformatics

Article Title: Current challenges and best-practice protocols for microbiome analysis

doi: 10.1093/bib/bbz155

Figure Lengend Snippet: A schematic overview outlining various experimental and computational challenges associated with 16S rRNA-based and shotgun metagenomic sequencing.

Article Snippet: At present, both Pacific Biosciences single-molecule real-time (SMRT) and Oxford Nanopore Technologies sequencing platforms are preferred due to their longer read sizes of 15–100 and ~1000 kilobases, respectively [ , ].

Techniques: Sequencing

Journal: Briefings in Bioinformatics

Article Title: Current challenges and best-practice protocols for microbiome analysis

doi: 10.1093/bib/bbz155

Figure Lengend Snippet: Major short-read and long-read sequencing technologies. ( A ) Illumina sequencing involves initial trimming, adenylation of the blunt ends and ligation of specific adapters to DNA molecules. Following this library, fragments are amplified in situ on flow cell surfaces through bridge amplification and produce sequencing clusters. Finally, reversible dye terminator sequencing step is implemented where single-nucleotide addition reactions and presence of blocking group at the 3′-OH (of the ribose moiety) help to identify sequencing clusters through a reporter fluorescent signal. ( B ) PacBio sequencing involves a circular consensus sequencing (CCS) SMRTbell technique. Herein, ligation of hairpin adapters to each end of a duplex DNA molecule forms a closed loop, which is sequenced in a zero-mode waveguide (ZMW), fluorescence-based readout of nucleotide incorporation. Each strand in the duplex DNA is sequenced together in multiple passes, and the consensus sequences from both strands are incorporated. ( C ) Nanopore sequencing involves ligation of hairpin adapters at one end of duplex DNA molecule before initiating nanopore sequencing of the linked original DNA strands. The blockades in ionic current through the nanopore are optimally quantified as DNA base sequences.

Article Snippet: At present, both Pacific Biosciences single-molecule real-time (SMRT) and Oxford Nanopore Technologies sequencing platforms are preferred due to their longer read sizes of 15–100 and ~1000 kilobases, respectively [ , ].

Techniques: Sequencing, Illumina Sequencing, Ligation, Amplification, In Situ, Blocking Assay, PacBio Sequencing, Fluorescence, Nanopore Sequencing

Journal: Briefings in Bioinformatics

Article Title: Current challenges and best-practice protocols for microbiome analysis

doi: 10.1093/bib/bbz155

Figure Lengend Snippet: Best-practice protocol for the acquisition and analysis of targeted amplicon and shotgun metagenomics data from sequencing to functional annotation. The basic flow of experimental steps followed by downstream preprocessing and analysis steps is shown. At each step, the optimal tools utilized during the process are shown as well. All scripts are available at https://github.com/grimmlab/MicrobiomeBestPracticeReview .

Article Snippet: At present, both Pacific Biosciences single-molecule real-time (SMRT) and Oxford Nanopore Technologies sequencing platforms are preferred due to their longer read sizes of 15–100 and ~1000 kilobases, respectively [ , ].

Techniques: Amplification, Sequencing, Functional Assay