COMPUTATIONAL SERVICES

 

RNA-seq allows quantification of transcripts in biological samples at a specific time point. RNA-seq enables researchers to track changes in gene expression profiles, post-translational modifications, SNPs or mutations over time or between treatment groups. Our team will consult with you on project-specific details and outline an appropriate experimental design and/or customize bioinformatics/data analysis. At Genomics Core, we help our collaborators to jump start their data exploration by performing various statistical analyses to produce publication-ready results, including sample correlation, PCA, differential gene analysis and functional annotation.

01

REGULAR BULK RNA-SEQ

STANDARD PACKAGE INCLUDES

TIER 1

(1) Gene count matrix (TPM/COUNT)

(2) QC summary table

(3) MultiQC report

TIER 2

(1) A HTML report which can be shared and opened in any modern web browser. All plots are resizable and interactive with click and drag zooming. The HTML report contained the following three sections.

  • Unsupervised Analysis: Explores the data patterns or cluster without grouping information.

    1. 2D and 3D principal component analysis (PCA) and sample correlation clustering plots.

  • Differential Expression Analysis: Identifies significantly differentially expressed genes between sample groups.

    1. Heatmap, MA plot, volcano plots

  • A List of Differential Expressed genes: Lists significantly differentially expressed genes between sample groups.

(2) KEGG/GO/GSEA or IPA analysis (EXCEL table and PDF plot for enriched pathway)

(3) Excel table for differential expression analysis (log2FC, average gene expression in compared groups, adjusted p-value, etc,.)

(4) (optional) WCGNA analysis

 

Exploring small RNA expression and function has led to some important discoveries about the regulation of gene expression in normal biological processes and disease states, and has even recently given rise to unique circulating biomarker signatures. Our analysis will include alignment, classification, quantification and functional annotation of all mapped reads.

02

SMALL RNA-SEQ

STANDARD PACKAGE INCLUDES

TIER 1

(1)QC Excel table

(2) Raw/Normalized expression Excel table

TIER 2

(1) Differential expression analysis

 

ATAC-seq (Assay For Transposase-Accessible Chromatin Sequencing) is a fast and sensitive high-throughput sequencing method for epigenomic profiling of open chromatin, DNA-binding proteins, and nucleosome position. Our analysis will detect regions of open chromatin, with annotations regarding genes contained within that region and how the regions signals may have changed between samples.

03

BULK ATAC-SEQ

STANDARD PACKAGE INCLUDES

TIER 1

(1) QC report

(2) Peak calling Excel table

TIER 2

(1) Peak gene annotation

(2) IDR analysis (if replicates applicable)

(3) differential abundance analysis

(4) pathway analysis

(5) motif scan

 

ChIP-seq combines chromatin immunoprecipitation (ChIP) with massively parallel DNA sequencing to study DNA-protein interactions. ChIP-seq is widely used for the discovery of the genomic location of transcription-factor binding and histone modifications in living cells. This epigenetic information is complementary to genotype and expression analysis. We are able to deliver a list of significant peaks that are annotated with the genomic locations and statistical information, such as width, number of reads, significance p-values, location relative to the nearest genes (distance to TSS), location within genes (exon, intron, UTR), and the binding motif found within the peak.

04

ChIP-SEQ

STANDARD PACKAGE INCLUDES

TIER 1

(1) QC report

(2) Peak calling Excel table

TIER 2

(1) Peak gene annotation

(2) IDR analysis (if replicates applicable)

(3) differential abundance analysis

(4) pathway analysis

(5) motif scan

 

WGBS (whole genome bisulfite sequencing) is the gold standard to study genome-wide methylation at single base resolution. WGBS enables to simultaneously observe the methylation patterns of all CpG, CHG and CHH sites present in the sample of interest.

Our Tier1 analysis includes alignment of bisulfite sequencing data to reference genome, determination of methylation status of CpG nucleotides, bisulfite conversion rate, biological replicates consistency, and several other QC metrics.

We also provide additional analysis on request, including differential methylation analysis, annotation with genomic regions, gene ontology term analysis and pathway analysis.

05

WHOLE GENOME BISULFATE SEQUENCING (WGBS)

STANDARD PACKAGE INCLUDES

TIER 1

(1) MultiQC report

(2) Bedgraph with CpG site

(3) Bedgraph with all C

(4) Summary QC table (alignment rate, conversion rate, etc,.)

TIER 2

(1) Differential methylation analysis

(2) Pathway analysis

 

Whole genome sequencing (WGS) is the next-generation sequencing technology for a rapid and low cost determining of the full genomic sequence of an organism. WGS enables identification of various kinds of sequence variation, including single nucleotide variation (SNV), insertion and deletions (indel), copy number variation (CNV) and rearrangement, and detection of their association with a disease or phenotype.

Whole exome sequencing (WES) enables researchers to focus their resources on genes that are most likely to have an impact on the phenotype or disease of interest. By scanning through the entire exome region of the genome, it leads to identification of relevant variants across a wide range of applications, including genetic diseases, cancer development, and population genetics.

We will provide variant analysis including high-quality mapping of raw reads data and summarizing SNPs, INDELs in your samples.

06

WHOLE EXOME/GENOME SEQUENCING (WES/WGS)

STANDARD PACKAGE INCLUDES

TIER 1

(1) raw SNP calling results (.vcf file)

(2) raw INDEL calling results (.vcf file)

(3) MultiQC report

TIER 2

Coming soon…

 

scRNA-seq enables a comprehensive, scalable solution for cell characterization and gene expression profiling of hundreds to tens of thousands of cells.

CITE-seq (Cellular Indexing of Transcriptomes and Epitopes by sequencing) combines highly multiplexed antibody-based detection of protein markers with unbiased transcriptome profiling for thousands of single cells in parallel. We uses in-house pipeline to analyze your CITE-seq data.

We put more effort to quality control and data visualization. Our service provide high quality report that clearly displays and analyzes single-cell expression patterns.

07

SINGLE CELL RNA-SEQ (including CITE-SEQ)

STANDARD PACKAGE INCLUDES

TIER 1

(1) Expression matrix (raw/normalized)

(2) Cloupe file for mRNA library(+multiplexing/Ab tags if applicable)

(3) QC report

TIER 2

Collaboration only, please contact genomics@cshs.org

 

Amplicon sequencing is performed to determine the relative abundance of each taxa in a community, and to compare taxonomic profiling between groups of interests. It enables researchers to address changes in the overall microbial profile over time, or between treatment groups.

08

MICROBIOME

STANDARD PACKAGE INCLUDES

TIER 1

(1) Biom format OTU abundance table

(2) QC report

TIER 2

Collaboration only, please contact genomics@cshs.org