Whole Genome De-novo sequencing
De novo sequencing refers to sequencing of a novel genome where there is no reference sequence available for alignment. GenePrint LifeSciences offer mate pair sequencing and long-read technology to complement shorter reads for comprehensive and accurate characterization of any species. Whole genome sequencing of any orphan genome starts with sequencing strategy development, library preparation, high throughput sequencing using a suitable NGS platform followed by genome assembly and advanced bioinformatics analysis. Whole genome de-novo assembly and annotation has the potential of unveiling the sequence of new genomes.
De novo sequencing provides useful information for mapping and sequencing genomes of novel organisms or completing genomes of known organisms. It generates accurate reference sequences for complex or polyploid genomes. It also clarifies highly similar or repetitive regions for accurate de novo assembly. Further, it can identify structural variants and complex rearrangements, such as deletions, inversions, or translocations.
Whole genome Re-sequencing
Whole genome re-sequencing means to sequence a genome whose reference sequence is already available. The name itself makes it clear that the objective of re-sequencing is to identify how an organism’s DNA sequence differs from the reference sequence. By comparing the sequenced genomes to the reference, a catalog of mutations specific to that individual is obtained, usually single nucleotide polymorphisms (SNPs) and insertions-deletions (indels), which could provide extremely valuable insights into the genetic background of the individual and the cause of a particular disease. Often this is associated with specific phenotypes based on which the individuals are selected. Additionally, with specifically planned experiments, large rearrangements (e.g., translocations, inversions, large copy number variations) can be also pinpointed through WGR. Whole genome re-sequencing starts with sequencing library preparation, high throughput sequencing using a suitable NGS platform followed by reference mapping and advanced bioinformatics analysis. GenePrint LifeSciences offers whole genome resequencing for any genome of your interest.
Various epigenetic modifications, including DNA methylation are known to regulate gene expression and are a subject of deep interest. Cytosine methylation can significantly modify temporal and spatial gene expression and chromatin remodeling. DNA methylation patterns are increasingly surveyed through methods that utilize massive parallel sequencing. Sequence-based assays developed to detect DNA methylation can be broadly divided into those that depend on affinity enrichment, chemical conversion, or enzymatic restriction. The DNA fragments resulting from these methods are uniformly subjected to library construction and massively parallel sequencing. The sequence reads are subsequently aligned to a reference genome and subjected to specialized analytical tools to extract the underlying methylation signatures. GenePrint LifeSciences offers next-generation sequencing (NGS) to uncover both genome-wide and targeted methylome sequencing that can provide researchers with insights into methylation patterns at a single nucleotide level. With whole-genome bisulfite sequencing, methylation status at practically every cytosine in the genome across most species can be analyzed.
Reduced Representation Bisulfite Sequencing (RRBS)
Reduced-representation bisulfite sequencing (RRBS-Seq) is a protocol that uses one or multiple restriction enzymes on the genomic DNA to produce sequence-specific fragmentation. The fragmented genomic DNA is then bisulfite converted and sequenced. This is the method of choice to study specific regions of interest. It is particularly effective where methylation is high, such as in promoters and repeat regions.
While limited to the repeatability of enzyme cut sites, RRBS can only cover CpG-rich regions, such as CpG islands and promoter regions. In disease research, DNA methylation pattern of promoters are closely related to gene expression and phenotypes. As a DNA methylation research method focusing on CpG-rich regions, RRBS can be used to study DNA Methylation difference among plenty of samples with smaller data.
MeDIP-Seq is a cost-effective method to study the whole genome DNA methylation based on immuno-precipitation. It can compare DNA methylation modification patterns between different cells, tissues and clinical samples efficiently, which is widely applied to study diseases and molecular breeding with large-scale samples. When the methylation analysis of only scientifically relevant regions is concerned, MeDIP is the method of choice. GenePrint LifeSciences offers Medip using your antibody and samples or immune-precipitated samples.
Whole Genome Bisulfite Sequencing
Bisulfite sequencing (BS-Seq) or whole-genome bisulfite sequencing (WGBS) is a well-established protocol to detect methylated cytosines in the genomic DNA. In this method, genomic DNA is treated with sodium bisulfite and then sequenced, providing single-base resolution of methylated cytosines in the genome. Upon bisulfite treatment, unmethylated cytosines are deaminated to uracils, which upon sequencing are converted to thymidines. Simultaneously, methylated cytosines resist deamination and are read as cytosines. The location of the methylated cytosines can then be determined by comparing treated and untreated sequences. Bisulfite treatment of DNA converts unmethylated cytosines to thymidines, leading to reduced sequence complexity. GenePrint LifeSciences has an expert team for whole genome bisulfite sequencing. Whole genome bisulfite sequencing is the gold standard method because of its single base resolution across the whole genome.
RIP-Seq (compare with Chip-seq) maps the sites at which proteins are bound to the RNA within RNA-protein complexes. In this method, RNA-protein complexes are immunoprecipitated with antibodies targeted to the protein of interest. After RNase digestion, RNA protected by protein binding is extracted and reverse-transcribed to cDNA. The locations can then be mapped back to the genome. Deep sequencing of cDNA provides single-base resolution of protein-bound RNA.
The key benefits of RIP-Seq are-maps specific to protein-RNA complexes, such as polycomb-associated RNAs. No prior knowledge of the RNA is required
RNA sequencing is the technique of choice when analysis of gene expression is the aim. While until recently, this was undertaken using microarray analysis, RNA sequencing has now completely replaced microarray. The main reason is that RNA sequencing is a direct analysis method and does not need replication. Moreover, it has the potential of identifying new RNA molecule in the target sample. GenePrint LifeSciences offers ref seq analysis, QC and curation of raw sequences, expression analysis with the list of unique sequences and annotation, and downstream gene expression analysis. Inter-sample analysis will be performed for identifying differentially expressed transcripts across the sample set.
Small RNA and miRNA Sequencing
Typical transcriptome sequencing projects have some small RNAs, but not a comprehensive coverage of small RNAome. Therefore, small RNA enrichment must be performed in order to have adequate representation of small RNAs. This is required when the main aim of the analysis is study of small RNAs. GenePrint LifeSciences offers deep sequencing of small RNA, which is followed by bioinformatics analysis for miRNA discovery and analysis. Data curation by removal of adaptor sequences, base calling, redundancy reduction, discovery of miRNAs, siRNA, snoRNA & piRNA etc, & quantitative analysis for determination of miRNA expression, length distribution, target prediction etc. would be performed.
Deep sequencing metagenome DNA samples and advanced bioinformatics analysis for microbial identification and analysis would be performed on practically any sample of your choice. 16S high-throughput methods show tremendous potential for identifying uncultivated or rare pathogenic agents, distinguishing shifts in the bacterial community associated with different states, understanding how microbiota are affected by the environmental factors, and differentiating between a core human microbial community from inter-individual variability.
Exons are the part of genes that code for amino acids, which ultimately makes a protein sequence. A large number of genetic diseases are due to mutations in the coding sequences, making it important to undertake coding sequence analysis. Total coding sequences across the whole genome are named as ‘exome’. Exome sequencing is commonly undertaken in clinical studies with an aim to identify the causative mutations. Extended exome also includes the sequencing of the splice sites as changes around these sequences affect the splicing and maturation of a gene product. We at GenePrint LifeSciences offer both exome and extended exome analysis with full scale analysis to identify genetic variations.
In a number of cases, we have intelligent guess and selected candidates for sequence analysis. Deep sequencing of targeted regions of interest in any genome is named as targetted resequencing. Targetted resequencing reduces the amount of data required for each sample and is an appropriate technique for genetic analysis in case-control studies aiming at large sample size. Target enrichment shall be done using long range PCR, Illumina Truseq Amplicon, Truseq Custom enrichment, Rain dance or Fluidigm Access Arrays based on the project requirement. You would be required to provide PCR products in case of targeted amplicon sequencing. GenePrint LifeSciences offers targeted resequencing of your amplified or fragment enriched samples.
Chromatin immunoprecipition (ChIP)
Chromatin immunoprecipition (ChIP) is a powerful technique to study interactions between protein and DNA in vivo. ChIP combining with high-throughput sequencing technology (ChIP-Seq) identifies binding sites of DNA-associated proteins efficiently and accurately, which is widely applied to study histone modification and transcription factors binding sites. Chip-Seq is the ideal technique for identification of protein binding sites on DNA and target identification for studying signaling. GenePrint LifeSciences offers Chip-seq with complete data analysis.