Quick Biology Inc.

MeRIP-Sequencing (RNA Methylation)

Alternative names: RNA Methylation Seq, MeRIP-Seq, N6-Methyladenosine Seq, M6A RNA-seq

RNA methylation is a reversible post-translational modification to RNA that epigenetically impacts numerous biological processes. It occurs in different RNAs including tRNA, rRNA, mRNA, tmRNA, snRNA, snoRNA, miRNA, and viral RNA. Different catalytic strategies are employed for RNA methylation by a variety of RNA-methyltransferases.

N6-methyladenosine (m6A) represents an abundant RNA modification that is conserved across many different species, ranging from plants, to yeast, to mammals. Similar to the 5-methylcytosine (5-mc) modification of DNA, m6A is a reversible chemical modification of RNA. m6A RNA modifications are an emerging topic in controlling cell fate transitions in mammalian embryonic stem cells. m6A is one of the most prevalent modifications on both mRNAs and noncoding RNAs in eukaryotes with an estimated 12,000 m6A sites in over 7,000 genes.

5-methylcytosine (5-mC) is an epigenetic mark that also commonly occurs in various RNA molecules. Researchers are able to bisulfite convert RNA, perform RT-PCR amplification, cloning, and sequencing to gain information about RNA cytosine methylation states. By treating RNA with bisulfite, cytosine residues are deaminated to uracil while leaving 5-methylcytosine intact.

Quick Biology now offers both MeRIP/m6A-seq and 5-mC RNA Bisulfite-Seq, please contact us to learn more!

Hi-C Sequencing

Please inquire about our new Hi-C seq service.

The three-dimensional (3D) conformation of genomes has a profound impact on gene regulation, DNA replication, and DNA damage repair. Recent years have seen a drastic expansion of genome conformation mapping technologies, including Hi-C, a sequencing-based assay designed to interrogate the 3D organization
of the genome. While existing Hi-C protocols have served as a tremendously valuable tool for some in the community, widespread adoption has been precluded by labor-intensive, cumbersome and complex protocols, prolonged ~4 day duration, inconsistent experimental results, and the demand for billions of sequence reads per sample for high-resolution chromatin looping analyses.

Quick Biology is now implementing a streamlined and simplified Hi-C sequencing workflow that produces high-quality libraries with consistency. The high quality and enriched signal-to-noise HiC library enables the identification of both known and previously unknown chromatin interaction loops at much reduced sequencing depths.

We are running a pre-launch trials now and will accpet projects with discounted pricing. Please inquire about our Hi-C seq service.

RNA seq

Sample requirements:

1) Total RNA amount: ≥ 1 ug for normal input; minimum 200 ng RNA input. Suspend RNA in RNase-free H2O.
2) Minimum sample concentration should be ≥ 20 ng/μl regularly.
3) RIN value ≥ 6.5 for plants and fungi, RIN value ≥ 7.0 for human and animals.
4) Purity: OD260/280 = 1.8-2.2, OD260/230 ≥ 2.0 without degradation or DNA contamination. Evaluate RNA integrity using a 1% denaturing RNA gel or an Agilent Technologies 2100 Bioanalyzer. Please submit your gel image or Agilent Bioanalyzer trace for your samples.
5) RNase-free screw-cap microcentrifuge tubes should be used for storage and shipping. Please label your samples clearly.

***: All information here is subject to change without notice. Please contact Quick Biology for latest pricing and terms.

We are specialized in doing single-cell (low-input) RNA-seq library preparation for FFPE/degraded/low-input samples including single cells. Single-cell methods include whole transcriptome amplification (WTA), Chromium 10X and UPX 3' single-cell mRNA-seq. Please ask for a quote.

Quick Biology’s single cell / low-input RNA-seq service (scRNA-seq) Option delivers:

Option #1 (low input/single-cell RNA-seq):
· Transcript discovery and differential expression from single eukaryotic cells and RNA-seq from limited samples including viral RNA.
· An all-in-one, direct cell-to-library solution incorporating robust whole transcriptome amplification (WTA) and highly efficient library preparations
· Completely PCR-free cell-to-library protocol to minimize bias and maximize transcript detection
· Libraries from single cells using a Quick Biology optimized streamlined protocol
· RNA-seq data includes both mRNA and lincRNA
· Fewer sequence errors – this is perfect for viral genome sequencing

Our scRNA-seq is suitable for transcriptome amplification for the analysis of:
(1) mRNA with poly A+ tails
(2) Total RNA
Note: Not recommended for tRNAs, miRNAs, severely degraded RNA, RNA from FFPE material or samples fixed by formaldehyde, glutaraldehyde or other fixatives.

Quick Biology scRNA-seq workflow:
We follow a complete WTA workflow from cell lysis, gDNA removal and cDNA synthesis to highly uniform amplification across the entire transcriptome in a one-tube protocol – with negligible sequence bias.

Sample requirements:
· 1–1000 intact cells from all vertebrate species (e.g., human, mouse, rat, sorted cells, tissue culture cells, cells picked under the microscope or microdissected cells from frozen tissue).
· 100 pg – 100 ng of purified RNA

Option #2: Chromium 10X single-cell transcriptome seq:
The Chromium Single Cell Gene Expression Solution provides a comprehensive, scalable solution for cell characterization and gene expression profiling of hundreds to tens of thousands of cells. Our latest improvements allow you to detect even more unique transcripts per cell and with the addition of Feature Barcoding technology, you can get a more complete molecular readout cell by cell—identify cell-specific CRISPR-mediated perturbations or simultaneously measure gene and cell surface protein expression in the same cell, with virtually unlimited possibilities for the additional feature types.
- Identify and characterize rare cell types
- Analyze and understand cellular heterogeneity and how this contributes to your biological system
- Perform cellular phenotyping with single cell RNA-seq to identify novel targets, biomarkers, and cell types and states without the need for pre-selected targets
- Evaluate mRNA and cell surface protein expression profiles within the same cell
- Perform high throughput and high resolution functional genetic screens in tens of thousands of cells simultaneously
- Assess comprehensive gene expression phenotypes for individual CRISPR perturbations

Option #3: Quick Biology’s UPX 3' single-cell mRNA-seq service (UPX 3' scRNA-seq) delivers:

• For high-throughput 3' transcriptome NGS from ultralow amounts of RNA
  
• Start with 1–100 cells or 10 pg to 1 ng of isolated RNA
  
• LNA-enhanced chemistry for increased accuracy, specificity and sensitivity
  
• UMIs eliminate library amplification bias for accurate gene expression
  
• UPX tagging allows 4608–18,432 samples per single sequencing lane
  

Sample requirements:
· start with 1–100 cell
· 10 pg to 1 ng of isolated RNA

Please check out our 2018 new service Single-cell/Low-input Whole Genome Sequencing!

We provide a complete solution for whole-genome sequencing from isolated single animal or bacterial cells or low amounts of genomic DNA (1–1000 intact cells, or >50 pg purified gDNA). This service is ideally suited to the analysis of aneuploidy and copy number variation and sequence variation in single cells or for whole genome sequencing from rare samples.

Applications:
- Analysis of inter-cellular genome heterogeneity
- Mutation detection
- Copy number variation analysis
- Aneuploidy analysis

Obtain whole genome sequences with comprehensive genome coverage and exceptional sequence fidelity from single cells or low input gDNA.
The proliferation of technologies that enabled the analysis of single, isolated cells has transformed research in neuroscience, cancer, reproduction and more. With technological breakthroughs in single cell isolation, whole genome amplification (WGA) and NGS library preparation, experiments using single cells are now possible – opening a wealth of exciting new insights for you to discover. However, challenges still exist. In particular, methods for the unbiased and complete amplification of a single genome and for the efficient conversion of that amplified DNA into a sequencer-compatible library face several technical limitations including incomplete amplification, the introduction of PCR errors, GC-bias and locus or allelic drop-out.
With these considerations in mind, Quick Biology offers optimized solutions for your research with the new low input / single cell whole genome sequencing (WGS) service.

Quick Biology’s single cell / low-input WGS service (scWGS) delivers:
• High sensitivity: Typical yield is greater than 5 µg when starting with 1 ng of genomic DNA. Whole genome amplification from as low as 6 pg DNA (5 human cells).
• Reduced amplification bias and no primer artefacts: Primer-free amplification method utilizes a combination of TthPrimPol Primase (to synthesize primers) and Phi29 DNA polymerase.
• Obtain higher genome coverage and greater sequence fidelity.

Quick Biology scWGS workflow:
We follow a complete WTA workflow from cell lysis, cDNA synthesis, highly uniform amplification across the entire genome to the final Illumina Sequencing in an optimized protocol:
Sample requirements:
• 1–1000 intact cells from many species (e.g., human, mouse, rat, bacteria, sorted cells, tissue culture cells, cells picked under the microscope or microdissected cells from frozen tissue).
• 50 pg – 1 ng of purified gDNA, free of any contaminants.

Turnaround time
About 4 weeks, depends on the quality of submitted samples, one additional week for data analysis.

Whole Exome Sequencing
Required at least 6 samples.
2*150 PE with Hiseq 4000
Depth 50x
Including capture/library preparation/Reads QC

***: All information here is subject to change without notice. Please contact Quick Biology for latest pricing and terms.

Human Whole Genome Sequencing (WGS) on HiSeq X Ten, 90Gb (~30x), Turn Around Time: 4-6 weeks, including:
(1) Library preparation & Sequencing (~30x coverage, ~90 Gb raw data /sample, (PE150, Q30 ≥ 80%))
(2) Analysis (Data quality control, Alignment with UCSC hg19, Variant (SNP, CNV, InDel and SV) calling, annotation and statistics; and Somatic variant detection if samples are paired).
(3) data delivery (raw FASTQ, and final report) via hard drive.

SAMPLE REQUIREMENTS:

1) DNA amount: ≥500 ng for normal input (PCR-free); minimum 200 ng
2) DNA concentration: ≥20 ng/μL, Optimal concentration: 20 ng/μl to 500 ng/μl in Tris-HCL (pH8.0).
3) Purity: A260/280:1.8-2.0, A260/230: ≥ 1.8, Intact DNA, RNA-free, and non-degraded.
4) DNase-free screw-cap microcentrifuge tubes should be used for storage and shipping. Please label your samples clearly.

***: All information here is subject to change without notice. Please contact Quick Biology for latest pricing and terms.

We offer very competitive pricing on ATAC-seq (Assay for Transposase-Accessible Chromatin with high throughput sequencing), which is an alternative or complementary method to MNase-seq (sequencing of micrococcal nuclease sensitive sites), FAIRE-seq and DNAse-seq. It aims to identify accessible DNA regions, equivalent to DNase I hypersensitive sites.

SAMPLE REQUIREMENTS:
1. If sending cells, prepare a cell pellet containing at least 1 x 10^5 cells (2.0 x 10^6 cells recommended). Please provide total cell number on the sample sheet.
2. Wash the centrifuged cell pellet with phosphate buffered saline (PBS) at least once (recommend three times) and place the cell pellet in a 1 ml vial or tube.
3. Resuspend the pellet in Cryostor media (or a compatible freezing media with DMSO). Freeze the cell vials at 80°C overnight slowly in an isopropyl alcohol chamber (aka Mr. Frosty) or similar cooling device at a rate of -1 degrees C per minute.
4. Label sample tubes with your company/institution name, sample identifier (such as cell line and passage), date of submission, and number of cells.
5. Ship the cell vials on dry ice, please see the sample packing recommendations for details.

We also offer Whole-Genome Bisulfite Sequencing, please quote!

We offer service in circular RNA sequencing for efficient detection of circular RNAs and their genomic location through NGS sequencing and bioinformatics analysis such as: identifying, annotating and visualizing circRNAs and comparing relative expression, De novo assembling novel circular RNA transcripts, and characterizing various of alternative,(back-)splicing events of circular RNAs, etc.

Quick Biology’s miRNA-seq service delivers:

· Comprehensive discovery and differential expression of miRNA from many sample types including biofluids, low input samples, FFPE and any tissue.
· Gel-free miRNA sequencing library prep from as little as 1 ng of total RNA
· Integrated Unique Molecular Indices (UMIs) enable quantification of individual miRNA molecules, eliminating PCR and sequencing bias
· miRNA-seq data includes both miRNAs and other small RNAs (piRNA)
· Bioinformatics solutions for differential expression analysis and discovery of novel miRNAs

Quick Biology’s miRNA-seq is suitable for small RNAs for the analysis of:
(1) Biofluids (such as serum, plasma, CSF and urine)
(2) Total RNA and miRNA
(3) Cells, fresh/frozen tissue and FFPE tissues
(4) Exosomes containing small RNAs

Sample requirements:
· Serum, plasma, cells, fresh/frozen tissue and FFPE tissues
· 100 ng – 500 ng (minimum 1 ng) of purified total RNA (please isolate RNA using kits that retain miRNA fractions)

Bioinformatics for miRNA Sequencing:

Standard Analysis:
a. Raw data QC and clean up
b. Alignment to a reference with mapping statistics
c. miRNA count, quantifications, and differential miRNA expression analysis
d. Downstream miRNA target analysis and clustering
f. Final project report (HTML) with analysis methods, publication-ready graphics, and references

Advanced Analysis:
Please inquire about Quick Biology's customized data analysis.

Turnaround time:
About 4 weeks, depends on the quality of submitted samples, one additional week for data analysis.

We offer a very competitive price and the highest data quality in the market. Please quote.

ChIP-sequencing, also known as ChIP-Seq or ChIP-seq, is a method used to analyze protein interactions with DNA. It combines chromatin immunoprecipitation (ChIP) with massively parallel DNA sequencing to identify the binding sites of DNA-associated proteins. ChIP-seq is used primarily to determine how transcription factors and other chromatin-associated proteins influence phenotype-affecting mechanisms. Determining how proteins interact with DNA to regulate gene expression is essential for fully understanding many biological processes and disease states. This epigenetic information is complementary to genotype and expression analysis.

Quick Biology is a professional ChIP-Seq provider and will ensure the customer to get the most out of the sequencing project.

Complete ChIP-seq from cells/tissue to sequence

• Input Amount of Tissue/Cells:
  In general, the number of cells and tissues for each reaction can be 1 x 10^5 to 1 x 10^6 and 5 mg to 50 mg, respectively. For optimal preparation, the input amount should be 4 to 5 x 10^5 cells or 20 to 30 mg tissues so that the amount of DNA enriched from the ChIP reaction can range from at least 1 ng to 100 ng.
  
• Starting Materials:
  Starting materials can include various tissue or cell samples such as cultured cells from a flask or plate, fresh and frozen tissues, etc.
  
• Antibodies:
  Antibodies should be ChIP-grade in order to recognize fixed and native proteins that are bound to DNA or other proteins.
  

If submitting ChIP-DNA fragments:

Sample requirements
• DNA amount quantified by Qubit 2.0: ≥ 100ng; minimum 10 ng
• DNA concentration: ≥1 ng/μL
• Total volume: ≥10 μL

Bioinformatics for ChIP Sequencing:

Standard Analysis:
a.Raw data QC and clean up
b.Alignment to a reference with mapping statistics
c.Peaking calling with or without control samples
d.Gene assignment and peak annotation
e.Pathway Analysis
f. Final project report (HTML) with analysis methods, publication-ready graphics, and references

Advanced Analysis:
h.Motif analysis
i.clustering and visualization

Turnaround time:
~3-4 weeks depending on project requirements, one additional week for data analysis

HiSeq X ten, PE150, yeild: >600 M reads; 90Gb of data
Hiseq 3000, SE50, yield: >300M reads; $1500 Per lane;
Hiseq 4000, PE150 , yield: >600 M reads; 90Gb; $2650 (was $3000) Per lane
NovaSeq 6000, S2 flow cell, yield: 6600M reads; 850–1000 Gb of data
NextSeq 500 options:
- PE 2x150 High Output (up to 800M reads)
- PE 2x150 Mid Output (up to 260M reads)
- PE 2x75 High Output (up to 800M reads)
- PE 2x75 Mid Output (up to 260M reads)
- SR 1x75 High Output (up to 400M reads)
MiSeq v2 and v3

SAMPLE REQUIREMENTS:
• Please contact us for compatibility of the library, Please provide index table if it is pooled library of many samples.
• Library amount and size: ≥ 70 x 10-3 pmol, The insert fragment size should be no more than 600bp. Single peak should be observed.
• Library concentration: ≥ 5 nM (fragment size adjusted), with volume range of 15-100 uL in Tris-HCL (pH8.0). Please label conc. clearly in tubes.
• Please provide QC analysis results measured by one or several of the following methods: Qubit®, NanoDropTM, Gel Electrophoresis, Caliper LabChip GX or Agilent Bioanalyzer.
• DNase-free screw-cap microcentrifuge tubes should be used for storage and shipping. Please label your samples clearly.

***: All information here is subject to change without notice. Please contact Quick Biology for latest pricing and terms.

Bioinformatic Service for RNA-seq
- Standard service:
a.Raw data QC and clean up
b.Alignment to a reference with mapping statistics
c.Gene and transcript-based quantitation, TPM/RPKM/FPKM-based quantitation, Raw hit count-based quantitation
d.Differentially Expressed Gene
e.Clustering
f.Gene Ontology
g.Pathway Analysis

• Advanced service:
  i.Alternative pre-mRNA splicing
  j.RNA editing
  k.Antisense transcript
  l.Novel transcripts
  m.Fusion genes/transcript detection
  Final project report with analysis methods, publication-ready graphics, and references
  

***: All information here is subject to change without notice. Please contact Quick Biology for latest pricing and terms.

HLA typing with Illumina TruSight HLA sequencing panel v2.
The Sequencing Panel covers all commonly typed HLA loci, plus those with emerging relevance:
Loci: Target Sequence
HLA-A: 4.1 kb (entire gene)
HLA-B: 2.8 kb (exon 1 — intron 6)
HLA-C: 4.2 kb (entire gene)
HLA-DRB1/3/4/5: 4.6 — 5.1 kb (exon 2 — intron 4)
HLA-DQB1: 6.9 kb (entire gene)
HLA-DPB1: 9.7 kb (exon 2 — 3' UTR)
HLA-DQA1: 7.3 kb (entire gene)
HLA-DPA1: 10.3 kb (entire gene)

Please inquire for a quote

Quick Biology is specialized in Sequencing projects.
We provide cost effective consultation on experimental design for sequencing project. Please send us the project details.

Illumina library preparation for RNA-seq, exome-seq, ChIP-seq and whole genome sequencing.
Start from $200 per sample.

***: All information here is subject to change without notice. Please contact Quick Biology for latest pricing and terms.

$170/sample (was $250/sample);
Our advanced bioinformatics analysis will guide your research smoothly from sample data to discovery. While other companies deliver massive amounts of NGS data in Excel or text file formats, we go much further with in-depth bioinformatics analysis and the delivery of analysis results in user project relevant context.

***: All information here is subject to change without notice. Please contact Quick Biology for latest pricing and terms.

Professional bioinformatics support has become an essential part of any NGS based Genomics study. Quick Biology’s bioinformatics service is designed to assist researchers in areas of difficulties, such as Bio-IT, statistics, and data mining.

We perform also perform microarray data analyses, which can be combined with NGS results. A lot of microarray data can be downloaded from public repository such as GEO and ArrayExpress.

Unique bioinformatics services from Quick Biology:

1.RNA-seq
a.Raw data QC and clean up
b.Alignment to a reference with mapping statistics
c.Gene and transcript-based quantitation, TPM/RPKM/FPKM-based quantitation, Raw hit count-based quantitation
d.Differentially Expressed Gene
e.Clustering
f.Gene Ontology
g.Pathway Analysis
h.Gene interaction network
i.Alternative pre-mRNA splicing
j.RNA editing
k.Antisense transcript
l.Novel transcripts
m.fusion genes/transcript detection
n.Final project report with analysis methods, publication-ready graphics, and references

2.Whole Exome Sequencing
a.Germline variants, compared to reference genome
b.Somatic mutations if Tumor-Normal pair (SNVs, InDel, CNV)

3.Whole Genome Sequencing
a.Germline variants, compared to reference genome
b.Somatic mutations if Tumor-Normal pair

4.ChIP Sequencing
a.Raw data QC and clean up
b.Alignment to a reference with mapping statistics
c.Peaking calling with or without control samples
d.Gene assignment and peak annotation
e.clustering and visualization
f.Motif analysis
g.Pathway Analysis
h.Gene interaction network analysis
i.Final project report with analysis methods, publication-ready graphics, and references

5.Combinatorial/Integrative Genomics and customized service
-Combinatorial
a.Combine with Cancer Genome Atlas: TCGA)
b.Combine with data in GEO (Gene Expression Omnibus)
c.Combine with data in ArrayExpress
d.Combine with data in Cosmic
e.Combine with data in GDSC
f.Combine with data in CCLE
-Integrative Genomics and customized service
g.Sequential analysis combining several distinct omics data from same set of samples.
h.Gene-set analysis to discover novel or using known groups of related genes/molecules.
i.Pairwise correlation analysis to infer molecular network interactions.
j.Network analysis using molecular network interactions to identify active or aberrant subgraphs.
k.Bayesian analysis to guide making correct assumptions to integrate multiple omics data.
l.Integrative analyses of many tumor types for clinical application.

Statistical Analysis Services

Data Analysis Services

Data Services