Default

BGI Genomics

12 Orders Completed
Cambridge, Massachusetts, US

About BGI Genomics

We Sequence, You Discover.

BGI was founded in 1999 to support the Human Genome Project. Since then, BGI has grown into a multinational genomics company with global operations, including sequencing laboratories based in the US, Europe, Hong Kong, and mainland China. · Next Generation Sequencing Services · Pharma R&D Solutions · Proteomics Services · Bioinformatics Services We operate all common NGS platforms, and exclusively offer the best data quality at the lowest cost from DNA Nanoball Sequencing with the DNBSeq system, developed by BGI’s Complete Genomics subsidiary. · The highest quality data · The quickest turn-around · The lowest cost Our vast experience with Genomics, Proteomics and Bioinformatics positions BGI uniquely to support academia and pharmaceutical companies with highly reliable genomic data for Basic Research and Drug Development. 

Our Services (13)


ic

De Novo Genome Sequencing

Price on request

Plant and Animal de novo Sequencing

Service Description

De novo sequencing refers to the sequencing of a novel genome without a reference sequence for alignment. The process of de novo genome sequencing involves the sequencing of small DNA fragments, assembling the reads into longer sequences (contigs) and finally ordering the contigs to obtain the entire genome sequence.

BGI is a recognized leader in de novo Whole Genome Sequencing and has extensive experience from the de novo sequencing and assembly of more than 100 species genomes. Currently over 70% of higher plant and animal genomes have been sequenced by BGI and its partners (including unpublished species).

We offer a complete suite of technologies to support your de novo sequencing projects, along with expert assistance with the planning of optimal sequencing and bioinformatics options, to assure your project is a success.

Sequencing Specification

BGI Plant and animal de novo services are executed with multiple sequencing systems

Sample preparation and services

• Library preparations (DNBSEQ™/Illumina, 10X Genomics, PacBio Sequel etc.)

• Various sequencing modes

• Raw data, standard and customized data analysis

• Available data storage and bioinformatics services

Sequencing quality standard

• Guaranteed ≥90% of clean bases with quality score of Q20

• Guaranteed ≥6G PacBio Sequel data with polymerase length longer than 10kb

Turnaround Time

• Typical 6 months for simpler genomes where only the NGS platform is used.

• Typical 25 working days for qualified DNA sample where only PacBio Sequel sequencing is used with no bioinformatics analysis required.

Project Workflow

We care for your samples from the start through the result reporting. Highly experienced laboratory professionals follow strict quality procedures to ensure the integrity of your results.

Sequencing Strategy

De novo sequencing usually requires a customized approach based on your subject species’ genome size and complexity as well as overall scientific objectives of the project.

Our plant and animal de novo sequencing service is usually performed using a combination of available platforms, including our own DNBseq™ technology NGS platform augmented with PacBio Sequel, BioNano Irys/Saphyr and 10X Genomics platforms for sequencing, library preparation and mapping. In addition, BGI offers extensive bioinformatics data analysis options for genome assembly, annotation and evolution.

Platform Tools

NGS: 170bp/350bp, 500bp-800bp,10X Genomics Chromium Library, PE100, PE250/126, PE150

PacBio Sequel: PacBio Sequel library (20kb), read length >10Kb

BioNano: DNA fragment size >250kb, ~1Mb mapping range

Our Sequencing specialists will work with you to design the optimal strategies for your project, using platform combinations as appropriate for your project:

Data Analysis

Besides clean data output, BGI offers a range of standard and customized bioinformatics pipelines for your plant and animal de novo sequencing project.

Reports and output data flies are delivered in industry standard file formats: BAM, .xls, .png. Raw FASTQ and FASTA data is available.

Standard Analysis

Data filtering

Available Advanced Analysis

Genome survey

K-mer analysis and genome size estimation

Heterozygous rate estimation

Genome assembly

Analysis of GC-depth distribution

Genome assembly

Assembly

Analysis of GC-depth distribution

Analysis of GC-content distribution

Analysis of sequence depth

Evaluation of autosomal regional coverage

Evaluation of gene region coverage

Annotation

Repeat annotation

Gene prediction

Gene function annotation

ncRNA annotation

Evolution

Gene family identification

Phylogenetic analysis

Estimation of species divergence time

Whole genome alignment

Whole genome duplication

Customized Analysis

Further customization of Bioinformatics analysis to suit your unique project is available: Please contact your BGI technical representative.

Sample Requirements

We can process your DNA sample of plants and animals with the following general requirements (Actual sample requirements for each specific project will depend on the number and type of libraries to be constructed). BGI also provide special sample extraction services to satisfy project requirements.

Libraries

Small Insert: 170/350bp, >1.5, ≥20

Mate Pair: 2kb-6kb, ≥10, ≥60 and 10kb, ≥10, ≥60

PacBio Library: 20kb, ≥13, ≥80

10X Genomics: Chromium library, ≥1, ≥20

BioNano: 4-6 /plug*, 40-200

 


ic

Small RNA Sequencing

Price on request

Service Description

Small RNAs are a type of non-coding RNA (ncRNA) molecule that are less than 200nt in length. They are often involved in gene silencing and post-transcriptional regulation of gene expression. Small RNA sequencing is used to discover novel small RNAs, examine the differential expression of all small RNAs and to characterize variations with single-base resolution.

Unique Molecular Identifier (UMI) Service Option

Unique Molecular Identifiers (UMIs) can be utilized to eliminate undesirable PCR duplicates derived from a single molecule. After PCR, molecules sharing a UMI are assumed to be derived from the same input molecule. As such, UMI counts offer superior results to counting reads, leading to more accurate estimates of quantitative small RNA expression[1]. UMI technology is especially beneficial to customers doing research on rare and precious samples or samples containing less RNAs, such as exosomes. Our DNBseqTM Small RNA sequencing service with optional UMI technology delivers accurate, affordable and high-quality sequencing data to support your academic and clinical research applications.

Sequencing Service Specification

DNBseqTM Small RNA Sequencing Services are performed with the DNBseqTM technology, featuring cPAS and DNA Nanoballs (DNBTM) technology for superior data quality[2].

• 50bp single-end sequencing reads

• Standard output 20 Million clean reads per sample

• Available UMI technology for enhanced quantification accuracy

• Clean data and bioinformatics analysis are available in standard file formats

• Standard and customized bioinformatics data analysis are available

• Cloud-based data storage and delivery system

Turnaround Time

• Typical 25 working days from sample QC acceptance to filtered raw data availability

• Expedited services are available, contact your local BGI specialist for details

Project workflow

We care for your samples from the start through to the result reporting. Highly experienced laboratory professionals follow strict quality procedures to ensure the integrity of your results.

DNBseqTM Sequencing Technology

DNBseqTM is an innovative high-throughput sequencing solution, developed by BGI’s Complete Genomics subsidiary in Silicon Valley. The system is powered by combinatorial Probe-Anchor Synthesis (cPAS), linear isothermal Rolling-Circle Replication and DNA Nanoballs (DNBTM) technology, followed by high-resolution digital imaging.

The combination of linear amplification and DNB technology reduces the error rate while enhancing the signal. The size of the DNB is controlled in such a way that only one DNB is bound per active site on the flow cell. This densely patterned array technology provides optimal sequencing accuracy and increases flow cell utilization.

Data Analysis

In addition to clean data output, BGI offers a range of standard and customized bioinformatics pipelines for your small RNA sequencing project. Reports and output data files are delivered in industry standard FASTQ, and Excel file formats with publication-ready tables and figures.

STANDARD BIOINFORMATICS ANALYSIS

• Data filtering

• Length distribution of small RNAs

• Analysis of common and specific sequences between two samples

• Small RNAs distribution across selected genome• Identification of rRNAs, tRNAs, snRNAs, snoRNAs, etc.

• Identification of repeat associated small RNAs

• Identification of small RNA sequences which could align to exon/intron

• Identification of known miRNAs by aligning to designated part of miRbase

• Analysis of the expression pattern of known miRNAs

• Classification of small RNAs into several categories based on customer preference

• Prediction of novel miRNAs and their secondary structures by Mireap and miRDeep from unannotated small RNAs

• Family analysis of known miRNAs

CUSTOM ANALYSIS

Further customization of Bioinformatics analysis to suit your unique project is available: Please contact your BGI technical representative.

Sample Requirements

We can process your human, plant, animal or microbial samples with the following requirement:

Regular sample: mass ≥1μgConcentration ≥50ng/μl, 15 μl, RIN ≥7.5 (plant/fungi)RIN ≥8.0 (human/animal)

FFPE RNA: mass ≥1μgConcentration ≥50ng/μl, 15 μl, RIN ≥2.0DV200 ≥30%

Small RNA of Plasma/serum/exosome: mass ≥20ngConcentration ≥2ng/μl, 10μl, N/A

Stable and High-Quality Data Performance

Technical reproducibility[3]

To demonstrate the high technical reproducibility of the DNBseqTM technology platform, six human brain samples, two heart samples and two blood samples were sequenced. Reproducibility was assessed by using six technical replicates of human brain sample (see Fig. 1). The median correlation between the six replicates was 0.98, and the 25% and 75% quantile were 0.98 and 0.99, respectively.

Expression distribution of miRNAs on DNBseqTM technology platform, HiSeq platform and Microarray[3]

Comparisons of the distribution of the sequencing reads in human blood samples on HiSeq to those on the DNBseqTM technology platform showed more even coverage of lower abundant miRNA species on DNBseq system, which facilitates the discovery of new miRNAs.

The diagram in the figure below demonstrates that 90.8% of all blood sequencing reads from the HiSeq match to one single miRNA. 98.6% Of all reads from the HiSeq match to the top 10 miRNAs. For the DNBseq, 93.1% of all sequenced reads match to the top 10 miRNAs. The remaining 6.9% of reads match to the rest of the miRNAs.

For the Agilent microarray system, the sum of all expression intensities was assumed to be 100% since microarrays show a saturation effect. One of the top-ten miRNAs, miR-451a, which is found in 0.8% of HiSeq reads and in 45.9% of DNBseq reads is the highest expression in microarrays with 37.2% of all expression counts.

Excellent agreement of known miRNA detection between HiSeq and DNBseqTM

The agreement of known miRNA detected from a human sample between two platforms is above 80% as demonstrated by the data below (Internal Data).

Identified known miRNA on DNBseqTM technology platform

Known miRNAs of different species were identified on both DNBseqTM and HiSeq platforms in an internal experiment, demonstrating that a consistently higher number of known miRNAs was detected on DNBseqTM, compared to the HiSeq platform. This data suggests higher detection sensitivity of miRNA for DNBseqTM technology.

 


ic

RNA Sequencing

Starting at $149.00 per sample
Service Description Transcriptome sequencing is used to reveal the presence, quantity and structure of RNA in a biological sample under specific conditions. Compared to hybridization-based RNA quantification methods such as microarray analysis, sequencing-based transcriptome detection can quantify gene expression with low background, high accuracy and high levels of reproducibility within a large dynamic range. In addition, transcriptome sequencing does not require an existing genome sequence and can detect mutations, splice variants and fusion genes that cannot be detected by microarrays.
Sequencing Service Specification BGI transcriptome sequencing services are executed with the DNBseq sequencing technology, featuring cPAS and DNA Nanoballs (DNB™) technology for superior data quality. Project workflow We care for your samples from the start to the result reporting. Highly experienced laboratory professionals follow strict quality procedures to ensure the integrity of your results.
Sample preparation and services • Multiple choices for mRNA enrichment and rRNA removal kits· • Stranded and non-stranded sequencing is available· • 100bp and 150bp paired-end sequencing options available· • ≥30 Million reads per sample recommended· • Raw data and bioinformatics analysis are available in standard file formats· • Advanced and custom bioinformatics data analysis· • Cloud-based data storage and delivery system
Sequencing Quality Standard • Guaranteed ≥80% of bases with quality score of ≥Q30 Turnaround time • Typical 30 working days from sample QC acceptance to filtered raw data availability· • Expedited service are available, contact your local BGI specialist for details
Data Analysis In addition to raw data output, BGI offers a range of standard and customized bioinformatics pipelines for your transcriptome sequencing project. Reports and output data files are delivered in industry standard file formats: FASTQ, BAM and Excel.
Standard Analysis • Quantitative expression profiles • Alternative splicing analysis • Fusion gene analysis • SNP and Indel detection • Time series analysis • Gene ontology analysis • Pathway enrichment analysis • Hierarchical clustering analysis • Protein-Protein Interaction (PPI) analysis • Fungal pathogenic gene annotation (for fungi) • Plant disease resistance genes annotation (for plant)
Sample Requirements We can process your total RNA, blood, cell line, FFPE, fresh frozen tissues and single cell samples from a variety of species, with the following general requirements:
Sample TypeSpeciesAmountConcentration (ng/uL)RIN/RQN Value28s/18sDV200
total RNAHuman≥200ng ≥20≥ 7.0≥1.0N/A

Human FFPE≥200ng ≥20N/AN/A≥30%

Mouse/Rat≥200ng ≥20≥ 7.0≥1.0N/A

Insect≥1μg≥40N/AN/AN/A

Other Animals≥1μg≥40≥ 7.0≥1.0N/A

Plant/Fungi≥1μg≥40≥6.5≥1.0N/A

Sample Type (Human)FFPEWhole BloodCell LineTissue
Requirement≥5 slides≥5 μm slice per slide≥1mL≥2X10^5 cells≥30mg
Low-input transcriptome sequencing is available.
Stable and High-Quality Data performance 1,072 samples were randomly selected from over 10,000 samples that were sequenced at BGI’s laboratory over a period of 6 months. The data output and data quality remained stable over that period. The average Q20 and Q30 scores were 97% and 89.5% respectively.
Request Information or Quotation Contact your BGI account representative for the most affordable rates in the industry, to discuss how we can meet your specific project requirements or for expert advice on experiment design, from sample to [email protected] www.bgi.com

Illumina Novaseq DNBSEQ-T7 DNBSEQ-G400 DNBSEQ-G50 DNBSEQ-G400 FAST Epigenetics Genomics Good Laboratory Practice 165 rDNA Sequencing 18S ChIP-Seq Exome sequencing miRNA-seq Next Generation Sequencing Sequencing data analysis MGI DNBSEQ-T7 all Show 17 more tags Show less

ic

Whole Exome Sequencing (WES)

Price on request

Service Description

For many applications, Whole Exome Sequencing is gaining popularity as a viable and cost-effective alternative for Whole Genome Sequencing. BGI has performed professional exome sequencing services for many years at several locations around the world, to support human and animal (rodents and monkeys) research and to benefit small and large-scale clinical trials and pharmaceutical drug developmental project.

Besides raw sequencing data output, BGI offers standard and custom bioinformatics services and suit your specific research needs.
Project Workflow We care for your samples from the start through to the result reporting. Highly experienced laboratory professionals follow strict quality procedures to ensure the integrity of your results Sequencing Service Specification BGI Human Exome Sequencing Service are performed with the DNBseq sequencing technology, featuring cPAS and DNA Nanoballs(DNB™) for superior data quality.
Sample preparation and services
  • Agilent Sureselect or BGI exome kit for library construction and enrichment 100bp paired-end sequencing options available.
  • Clean data and advanced bioinformatics analysis are available in standard file formats
  •  Standard and custom bioinformatics data analysis
  • Available data storage and bioinformatics applications
Sequencing Quality Standard
  • Guaranteed ≥80% of bases with quality score of ≥Q30
  • Standard sequencing coverage ≥50X; ≥100x is recommended for cancer samples.
  • Turn Around Time
  • Typical 30 days after sample acceptance for data delivery
  • Expedited services are available, contact your local BGI specialist for details.

Data analysis Besides clean data output, BGI offers a range of standard and customized bioinformatics pipelines for your whole exome sequencing project. Reports and output data files are delivered in industry standard file formats: BAM, .xls, .png
Standard Bioinformatics Analysis
  •  Filtering
  • Alignment
  • SNP calling and annotation
  • SNP databases analysis
  • SNP functionality and conservation prediction
  • Statistics of SNP distribution on each gene functional element
  • InDel calling and annotation
  • InDel databases analysis
  • Statistics of InDel distribution on each gene functional elements
  • Cancer Somatic Mutation analysis
  • Population genetics analysis
  • Complex disease analysis
  • Mendelian disease analysis
  • De novo mutation analysis for family samples
Customized Analysis Further customization of Bioinformatics analysis to suit your unique project is available: Please contact your BGI technical representative
Sample Requirements We can process your gDNA, Blood, Cell line, Fresh frozen tissue samples from a variety of species, with the following general requirements:

Agilent SureSelect

ic

ChIP-Seq

Chromatin Immunoprecipitation Sequencing
Price on request

ChIP-Seq, also known as ChIP-Sequencing, is widely used to analyze protein interactions with DNA. It combines chromatin immunoprecipitation (ChIP) with massively parallel DNA sequencing to identify binding sites of DNA-associated proteins, and can be used to precisely map global binding sites for any protein of interest. ChIP sequencing offers higher resolution and more precise and abundant information in comparison with array-based ChIP-chip.

Benefits:

  • Wide detection range: Genome wide protein DNA interaction studies
  • Cost-effective: Less data required for identifying the binding sites in whole genome
  • Only require low amount of ChIP DNA: As low as 5ng ChIP-ed DNA is adequate

Bioinformatics:

  • Standard Bioinformatics Analysis
    • Data filtering (removing adaptor sequences, contamination and low-quality reads from raw reads)
    • Reads Alignment
    • Genome-wide distribution of ChIP sequencing reads
    • Genome-wide peak scanning and distribution
    • GO function analysis of peak-related genes
    • Difference analysis of multi-samples
    • Tag detection near transcription start sites
    • UCSC Genome Browser instruction
  • Advanced Bioinformatics Analysis
    • ChIP sequencing reads distribution around transcription start sites
  • Custom Bioinformatics Analysis
    • We can also perform customized analysis to meet specific needs of your projects.

Sample Requirements:

For the ChIPed DNA samples you need provide:

  • Purity: OD260/280=1.8-2.0
  • Concentration: ≥1ng/μl.
  • Basic Requirements:
    • Gel electrophoresis analysis result should be provided to make sure that the size of DNA fragments is between 100bp to 500bp, and most of the fragments should be about 250bp.
    • DNA total amount ≥10ng (although 5ng is acceptable, the greater the amount, the better) for every single library preparation.

For the cell line samples you need provide:

  • Cell numbers (for single round of ChIP enrichment): 5×107 cells for the species whose genome size is similar to human.
  • Antibodies for ChIP enrichment:H3K4Me3, H3K4Me2, H3K9Me3, H3K9Me2,H3K27Me3, H3K27Me2, and other necessary antibodies are acceptable after evaluation.


ic

Low Input/Single Cell Whole Genome Sequencing

Price on request

Single cell RNA-Seq enables transcriptome heterogeneity study at the resolution of a single cell. It also unlocks the spatial-temporal gene expression profile with cell-by-cell resolution, which is unarchivable by standard, bulk RNA sequencing. At BGI we provide high-throughput single cell gene expression profiling service using 10x Genomics Chromium Single Cell Platform to unveil 3’ end counting of mRNA transcripts. Our turn-key solution (cell/tissue-to-report) and premade library service (library-to-data) for Single cell RNA-Seq provide flexible tool set for you depending on your preference, equipment accessibility and schedule.

BGI’s Single Cell Sequencing Solution utilizes the 10x Genomics® Chromium™ system for sample prep and library construction. Sequencing of the single cell libraries can be conducted on our proprietary DNBSEQ™ platform to ensure the downstream service quality, or the Illumina® platform (HiSeq and NovaSeq) by customer’s preference. BGI also provides sequencing services for customer self-prepared libraries using 10x Genomics® Chromium™ system Single Cell 3′ Library Construction Kit v3 and Next GEM Single Cell 3’ Library Construction Kit v3.1.


ic

Illumina Sequencing

Price on request

HiSeq X/4000/2500/Novaseq

HiSeq2000 was launched as a new sequencing instrument by Illumina, Inc. in 2010, with the same principle as Genome Analyzer, using a stable reversible terminator sequencing-by-synthesis method. The technology uses four kinds containing terminal blocking group and different fluorescent signal bases to complete complementary strand synthesis, not only to ensure the high accuracy and sequencing order, but also to exclude the sequencing error caused by the repeat sequences and the homopolymer. Unlike Genome Analyzer, HiSeq2000 combines the optical systems and manufacturing processes, uses two laser sources on the Flow Cell Scan, at the same time, four cameras on the four kinds of bases were recorded to reduce signal interference between different bases improved sequencing accuracy. HiSeq2000 adopts dual surface imaging technology, Flow Cell effective area increased, thereby increasing the throughput, reducing sequencing costs.

Performance Parameters:

Read Length Single Flow Cell Output Single Flow Cell Run Time Dual Flow Cell Output Dual Flow Cell Run Time
1×35 47-52Gb 1.5 days 95-105Gb 2 days
2×50 135-150Gb 4.5 days 270-300Gb 5.5 days
2×100 270-300Gb 8.5 days 540-600Gb 11 days
Performance 2×50bp Q30≥85%, 2×100bp Q30≥80%

*Install specifications for HiSeq sequencers with an Illumina PhiX library and cluster densities between 610-678 K/mm2 that pass filtering on a HiSeq system using TruSeq v3 Cluster and SBS kits for HiSeq. Performance may vary based on sample quality, cluster density, and other experimental factors.

Technical Features:

  1. Dual surface imaging technology;
  • Four cameras were taking pictures of four kinds of bases, reducing signal interference;
  • After HiSeq2000 v3 reagents upgrade, Flow Cell width of each lane widening, increased the Flow Cell area; Cluster generation reagents upgrade reduces occur of GC bias during sequencing.

Illumina HiSeq2500

HiSeq2500 (the upgraded version of Illumina HiSeq2000 sequencing instrument) was launched in 2012. There are 20 Hsieq2500 in BGI and distributed around the world. Compared with HiSeq2000, HiSeq2500 has two sequencing modes: High Output mode and Rapid mode. High Output mode has the same pattern as HiSeq2000 sequencing instrument; there is no change in sequencing reagents and Flow Cell. Rapid mode uses the new Flow Cell and sequencing reagents, shortening sequencing time, sequencing read lengths up to 150bp.

Performance Parameters:

High Output Mode*

Read Length Dual Flow Cell Single Flow Cell Dual Flow Cell Run Time
1×36 95-105Gb 47-52Gb 2 days
2×50 270-300Gb 135-150Gb 5.5 days
2×100 540-600Gb 270-300Gb 11 days
2×150 - - -
Performance 2×50bp Q30≥85%, 2×100bp Q30≥80%

Rapid Mode*

Read Length Dual Flow Cell Single Flow Cell Dual Flow Cell Run Time
1×36 18-22Gb 9-11Gb 7 hours
2×50 50-60Gb 25-30Gb 16 hours
2×100 100-120Gb 50-60Gb 27 hours
2×150 150-180Gb 75-90Gb 40 hours
Performance 2×50bp Q30≥85%, 2×100bp Q30≥80%, 2×150bp Q30≥75%

*Install specifications based on Illumina PhiX control library at supported cluster densities (between 610-678 K clusters/mm2 passing filter using TruSeq v3 or 700-820 K clusters/mm2 passing filter using TruSeq Rapid kits). Run times for rapid run mode correspond to onboard cluster generation(1.5 hours) and sequencing; for high-output mode, run times correspond to sequencing only, not include Flow Cell Preparation time(4-5hours). Performance may vary based on sample quality, cluster density, and other experimental factors. HiSeq2000 instruments prior to serial number 700895, rapid mode to extend the running time of approximately 15 hours when upgraded.

Technical Features:

  1. Rapid mode uses 2 lane Flow Cell and new sequencing reagents, sequencing time is shortened to a few hours, the sequencing read lengths up to 150bp;
  • Dual flow path, supporting high output and rapid sequencing modes;
  • Deselect lanes to bypass image process, reduce scan time
  • Complete 1 human genome sequencing in one day.

Illumina Miseq

Miseq (Illumina) is a new generation of miniaturized sequencing instrument (bench-top) launched on February 2011, which uses a chemical method based on Illumina TruSeq technology that nucleotide sequencing-by-synthesis by reversible terminator. Compared with Hiseq2000, the unparalleled accuracy of next-generation sequencing reagents, transitory sequencing time by new fluid system are the main advantages, although the throughput of a run is low.

Performance Parameters:

Read Length Run Time Throughput Quality
2×150bp About 24 hours 4.5-5.1Gb Q30>80%
2×250bp About 39 hours 7.5-8.5Gb Q30>70%

Explanation:

(1)The above performance is based on Miseq sequencing V2 reagent. V1 reagent only supports 2x150bp, runs about 27 hours, 1.5-2Gb throughput, Q30>80%. But V1 reagent is no longer ordered.

(2)This data is based on Illumina control libraries PhiX (a balanced representation of A, T, G, and C nucleotides). The appropriate clusters density is 900-1200K/mm2, and 880-965K/mm2 after PF. But different sample sequencing results by their own properties.

Technical Features:

  1. Short sequencing cycle: Miseq V2 150PE is short to 24 hours running time, so it can used for fast and efficient amplicon sequencing and small genome sequencing, with a small amount of time to complete projects of small amount of data.
  • Up to 250bp of paired-end read-length:Miseq sequencing read length has reached 2x250bp, which can effectively across complex genomes highly repetitive regions,thereby enhancing the effect of assembly, more conducive for gene annotation and gene function dig.
  • Convenient sequencing process: Miseq is a compact, integrated platform for integration of cluster generation, Pair-end sequencing and complete data analysis, saving laboratory space. Through an intuitive touch-screen interface to carry out simple instrument operation, plug and play reagent with RFID tracking, with automated convenience.


ic

Metagenomics

Price on request

Metagenomics is the study of genomes contained within an entire microbial community. This technology has opened up a new era in the study of microbial diversity with direct access to the genomes of numerous non-cultivatable microorganisms in their natural habitat. Metagenomic sequencing analyzes microbial community diversity, gene composition and function, as well as metabolic pathways associated with the specific environment. This approach has been applied to environmental studies as well as biomarker research.

Benefits:

  • Comprehensive: Enable investigation of all microbes of a certain environment in a single experiment, as well as analysis of microbial community diversity and gene function
  • Short Turnaround Time: Rapid acquisition of microbial information compared to traditional methods that investigate individual strains

Bioinformatics Analysis:

  • Data processing
    • Remove adapter pollution
    • Remove low-quality reads
    • Remove host contamination (if any)
    • Data statistics
  • Metagenome assembly
    • k-mer analysis to evaluate the sequencing depth for each sample before assembly
    • GC-depth analysis with mapped reads after assembly
  • Analysis of species composition and abundance
    • Statistics of clean reads alignment to the known bacterial, fungal, and archaea genome databases
  • Genome components analysis
    • Gene prediction (towards those contigs of length ≥ 500 bp)
    • Prophage detection
    • Transposable elements (TEs) detection
  • Generate non-redundant gene catalog
  • Gene functional annotations
    • Gene functional annotation based on the KEGG (Kyoto Encyclopedia of Genes and Genomes) database
    • Gene functional annotation based on the CAZy (Carbohydrate-Active Enzymes Database) database
    • Gene functional annotation based on eggNOG (Evolutionary Genealogy of Genes: Non-supervised Orthologous Groups) database
    • Antibiotics resistance factors annotation based on ARDB (Antibiotic Resistance Genes Database)
  • Comparative analysis among samples (Sample groups ≥ 2, samples in each group ≥ 10)
    • Screening factors (species or function) significantly correlated with sample grouping
    • Principal component analysis (PCA) based on significant factors
    • Clustering based on significant screened factors
    • Customized analysis (case by case)

Specific custom analysis will be determined based upon customer requirements.

Sample Requirements:

  • Sample type: genomic DNA
  • Sample quantity: ≥ 2µg
  • Sample concentration: ≥30 ng/µL

Turnaround Time:

The standard turnaround time for the whole workflow (including library construction, sequencing and bioinformatics analysis) is 40-70 business days.

Completion Criteria:

Generate 1G clean data at minimum


ic

Low Input/Single Cell RNA Sequencing

Price on request

Scientific research through traditional transcriptome analysis of early-stage embryos, stem cells, cancers, immune cells, and developing neurons is limited, because the amount of sample that is obtained does not meet the minimum requirements for traditional NGS, which is probably due to extremely little or immensely high heterogeneity. Thus, the need for single-cell transcriptome analysis is particularly urgent. Single-cell RNA-Seq quantifies the mRNA of a single cell through single-tube reverse transcription and PCR amplification, allowing several micrograms of cDNA to be collected for traditional library construction and Hiseq2000 sequencing. Single-cell RNA-Seq is a novel application of RNA-Seq that is capable of sequencing a single cell or infinitesimal amounts of sample.

Benefits:

  • Accommodates an infinitesimal amount of sample input, which is not possible with traditional sequencing protocols.
  • Single-tube amplification greatly reduces sample loss. This benefit allows a minimum amount of sample to be required, ensures high sensitivity for library construction, avoids the loss of transcripts that are expressed with low abundance, and reduces data bias.
  • Provides reliable data for subsequent analysis.
  • More than 90% of genes can be detected.
  • A greater number of low-abundance transcripts can be detected than using microarray.
  • The technique is highly repeatable.

Bioinformatics Analysis:

  • Standard Bioinformatics Analysis
    • Data filtering includes removing adaptors, contamination, and low-quality reads from raw reads
    • Assessment of sequencing (statistics of raw reads, sequencing saturation analysis, and analysis of the distribution of reads for a reference gene)
    • Gene expression annotation (gene coverage, sequencing depth, etc.)
    • Differential gene expression analysis (two or more samples should be provided)
    • Expression pattern analysis of differentially expressed genes (DEGs)
    • Gene ontology enrichment analysis of DEGs
    • Pathway enrichment analysis of DEGs
  • Customized Bioinformatics Analysis
    • We can perform other customized analyses to meet the requirements of specific projects.

Sample Requirements:

Singe-cell sample

Level Sample Results
Level A Mammalian oocyte, single blastomere from one-cell stage to eight-cell stage (e.g. single cell of human/mouse early-stage embryo) Has been tested, success rate > 90%
Level B Single mammalian cells from morula to blastula; both free single cells and cell lines with diameters greater than 10 μm (e.g. circulating tumor cells) No test has been performed; theoretically executable with relatively low risk
Level C Normal tissue cells No test has been performed; lacks theoretical support, therefore high risk
Level D Special tissues/structural cells, e.g. cells from vegetative pole of ovipara Has been tested,impracticable

RNA sample

  • Sample condition:Integrated total RNA samples (no mRNA isolation). Avoid protein contamination during RNA isolation.
  • Sample quantity (for library construction once): total RNA ≥ 10 pg
  • Sample concentration: ≥ 10 pg/μL

Turnaround Time:

The average turnaround time for RNA-Seq on 50 cells is about 40 workdays.

Completion Indicator:

Completion is indicated by the number of clean reads. The goals are individualized for each project.


ic

Single Cell DNA Sequencing

Price on request

Single cell sequencing can facilitate the elucidation of cell lineage relationships. The major applications of this technique include profiling scarce clinical samples (i.e. circulating tumor cells), pre-implantation genetic diagnosis, embryonic development research, and tumor progression analysis.

Advancing the possibilities of single cell sequencing in human disease research, we have developed an innovative end-to-end solution for genomics analysis at the single cell level. Within this solution, multiple displacement amplification (MDA) has been further enhanced and incorporated into BGI’s whole genome amplification (WGA) protocol, which enables uniform amplification of genomic DNA from single cells (from as little as one cell) with negligible sequence bias and maximized genome coverage.

BGI has sequenced hundreds of cells, and the results from applying the new single-cell sequencing method to identify the genetic characteristics of essential thrombocythemia and clear cell renal cell carcinoma have been published in the journal Cell.

Benefits:

  • Less quantity of input DNA required
  • Longer length of amplified product (>10 kb), which is better for CNV and SV detection
  • High accuracy of amplification (error rate is 10-6-10-7)
  • High coverage: >95% bases can be targeted
  • Strict quality control: a QC step is measured by detecting housekeeping genes of WGA products to ensure comprehensive coverage and unprecedented low bias

Applications:

  • Variants calling at the single cell level
  • Pre-implantation genetic diagnosis (PGD)
  • Measuring intra-tumor heterogeneity and guiding chemotherapy
  • Clone evolution analysis during tumor progression

Bioinformatics:

  • Standard Bioinformatics Analysis
    • Data filtering (removing adaptors, contamination, and low-quality reads from raw reads)
    • Alignment and summary of data production
    • SNP calling, annotation, and statistics
    • InDel calling, annotation, and statistics
    • CNV calling, annotation, and statistics (only for whole genome resequencing)
    • SV calling, annotation, and statistics (only for whole genome resequencing)
  • Custom Bioinformatics Analysis
    • We can also perform customized analysis to meet requirements of specific projects, e.g., sub-clone evolution of tumor.

Sample Requirements:

  • Fresh Tissue: A size of 1-2 cm3 is recommended; as low as 5 mm3 is also acceptable for precious samples. Tissue samples should be immediately stored in liquid nitrogen or at -80 ℃ after surgical resection, without other solvents treatment.
  • Whole Blood (or Bone Marrow): The total volume should be no less than 5 ml. Samples should be collected with anticoagulant tube and stored at -80℃.
  • Cell Suspensions: No fewer than 100,000 cells are recommended. It is necessary to follow the standard cell cryopreservation operation protocols, freeze cells gradually with cryopreservation media, and store them in liquid nitrogen or at -80℃.
  • Isolated Single Cells: Single cells should be stored separately in 3-5 μL solvent (e.g., PBS), in DNase/Rnase free PCR tube (200 μL), and stored at -80 ℃ for no longer than one week. Cells should be free of nucleic acid–binding dyes.

Sequencing Strategy:

91 PE or 101 PE

Recommended Data Amount:

≥ 30X for whole genome resequencing. Sequencing depth can be customized according to the research purpose.

Turnaround Time:

The standard turnaround time for the workflow is approximately 57 business days for whole genome sequencing of 100 samples at 30X coverage.

Completion Indicator:

Effective mean depth of each sample should be no less than required in the contract.

10x Genomics Chromium System

ic

Protein-Protein Interaction Analysis

Price on request
Request a quote for more information about this service.

ic

DNA Methylation Analysis

Price on request
Request a quote for more information about this service.

ic

Genotyping and Gene Expression Assays

Price on request
Request a quote for more information about this service.

Not finding what you're looking for?

Get info on this provider's capabilities without requesting a quote.
LH

Lisa Huang

Director, Business Development
  • Positive review for RNA Sequencing:

    August 2018

    "very good service!"

BGI Genomics has not received any endorsements.