www.lcsciences.com 1-888-528-8818

microRNA Discovery & Profiling Services

Degradome Sequencing Service

Degradome sequencing provides a comprehensive means

of analyzing patterns of RNA degradation. Because

microRNAs can cause endonucleolytic cleavage of mRNA

by extensive and often perfect complementarity to

mRNAs, degradome sequencing has been used to identify

microRNA cleavage sites. Degradome sequencing has

confirmed many known and revealed novel plant

microRNA targets.

microRNA Sequencing Service

LC Sciences provides a comprehensive sequencing

service utilizing Illumina’s high-throughput sequencing

technology which enables comprehensive, highly

sensitive and specific discovery and profiling of all forms

of small RNAs in your sample. Profiling is transcriptome

wide - you can investigate all microRNAs, of any size,

known and unknown, in your sample.

microRNA Profiling Microarray Service

A cost-effective expression profiling service offering the

latest probe content and standard microarrays available

for every organism in the miRBase sequence database.

Flexible µParaflo® microfluidic biochip enables custom

arrays for profiling non-model species, validation of

computational predictions, and sequencing data follow-

up.

Seq-ArraySM Services

Seq-ArraySM provides an efficient pathway from an initial

broad microRNA search to focused biological insights.

Deep sequencing is performed to generate a

comprehensive atlas of all possible microRNAs for your

species/system. A custom microarray is designed based

on the bioinformatics analysis of the above results and

your specific research goals.

The study of microRNA is growing rapidly as researchers discover

new microRNAs and uncover the importance of these small

regulatory elements linked to a wide range of biological functions.

The miRBase sequence database is the primary public repository

for newly discovered microRNAs and the number of miRBase

entries has grown rapidly from a mere 218 in 2002 to almost

30,000 in the latest version, suggesting the existence of many

more microRNAs yet to be discovered.

Contributing to the rapid rate of new discoveries is the

development of several new advanced technologies such as high-

throughput sequencing and custom microfluidic arrays. The

increasing availability of these technologies makes the discovery of

new sequences in lesser understood organisms now routinely

possible. A straightforward process of discovery, confirmation, and

validation is commonly employed.

LC Sciences Comprehensive Services

Novel small RNA discovery

Isoform level expression profiling

Sequencing Degradome Microarray

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LC Sciences offers a complete suite of microRNA analysis services giving all researchers access to the latest

technologies that are enabling discoveries in this exciting field of biology. Our services now include: microRNA

sequencing for discovery and digital expression profiling applications, microRNA detection microarrays for

differential expression profiling and validation/confirmation of the newly discovered microRNAs, and

degradome sequencing for identification in plants and some animal species.

These comprehensive services are designed to be one-stop and produce the results needed to quickly advance

your biological and biomedical research. Our “Total RNA to Data” services include: sample QC, sample

preparation, microRNA analysis, bioinformatics analysis, and customer data report.

LC Sciences has extensive experience with microRNA analysis and related bioinformatics services. We were the

first provider of microRNA microarray services back in 2005 and we have processed thousands of samples to

date. This experience examining varied microRNA datasets gives us unique insight into microRNA research.

Our microRNA discovery and analysis customers have been publishing routinely since we began offering

services back in 2005. Numbering over 1000 now, these studies by leading researchers in the field contribute

to a fast growing body of knowledge defining this recently discovered class of regulatory RNAs.

Considering the time, labor, and materials it takes to perform these analysis experiments yourself, our

comprehensive services, performed by experienced staff, are a very economical option.

Go With Experience

Proven Reliability

Comprehensive Analysis

Cost Effective Solution

One-Stop Service

LC Sciences is dedicated to helping you design meaningful experiments, providing

reliable analysis services, and delivering the high-quality results needed to keep your

research moving toward discoveries. Please don’t hesitate to contact us if you need

help with your experimental design or have any questions about any of our services.

Cost-efffective, high throughput

differential expression profiling

microRNA target identification (in plants)

microRNA Discovery Sequencing Service

microRNA sequencing is a new method and a powerful tool to identify and

quantitatively decode the entire population of microRNAs in your sample.

microRNA Sequencing Profile microRNA in any species - there is no need for probes based on prior

sequence or secondary structure information.

Profiling is transcriptome-wide - investigate all microRNAs, of any size, known and

unknown, in your sample.

Achieve digital transcript expression analysis at the isoform level

Discover novel small RNAs.

Our Comprehensive Service LC Sciences provides a microRNA discovery service using Illumina’s high-throughput

sequencing technology which enables comprehensive coverage, highly sensitive and

specific discovery and profiling of all forms of microRNAs in your sample.

This service is comprehensive - from sample to data, providing advanced technology

and years of experience in efficient discovery and profiling of microRNAs.

Our “Total RNA to Data” comprehensive service includes: sample QC, sample

preparation (small RNA selection, library preparation, single molecule clonal

amplification), high-throughput sequencing, high-level bioinformatics analysis, and

customer data report.

Down-stream profiling of identified microRNAs (and other customer defined target

microRNAs) is also available by custom microarray services.

Data Analysis / Results We can generally have data back to you about 6 weeks from the date we receive your

total RNA sample.

Bioinformatics Package Includes:

Raw sequencing data – either FASTA-A or FASTA-Q files with base-calling quality

scores

LC Sciences analysis and quality filtering - processed data is reduced to mappable

reads

Custom construction of reference database(s) - miRBase, genome, etc and

mapping of all quality reads

Alignment, classification, & functional annotation of all mapped reads

Biostatistical analysis – expression analysis, multi-parameter data analysis, length

distribution, transcript copy number comparisons, etc

microRNA target prediction

microRNA target GO and KEGG enrichment analysis

Customer data report – includes a summary of methods and statistical analysis

(713) 664-7087 1-888-528-8818 Fax (713) 664-8181 info@lcsciences.com www.lcsciences.com

Illumina Hi-Seq Ultra High-Throughput Sequencing Platform

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The HiSeq is a powerful ultra-high-throughput sequencing system that enables a broad range of applications and study sizes.

Our lab routinely offers sequencing in the

100 bp PE and 50 bp SE configurations.

microRNA Profiling Microarray Service

Cost Effective 1-Stop Solution

A comprehensive microRNA expression profiling service to save you time, labor and

material costs. From your total RNA sample through data analysis in about two

weeks. In-depth data analysis includes all t-Tests, ANOVA and heat maps to get you

the information you need. Complex multi-array experiments are no problem for our

experienced technical team. Includes high level technical support.

Microfluidic Array Platform

These are not spotted arrays! A proprietary µParaflo® microfluidic biochip is used

and probes are produced by direct synthesis on the chip. The microfluidic technology

produces a uniform distribution of the sample solutions on the array and enhances

binding reactions and stringency wash processes.

The microarray chip consists of thousands of three-

dimensional chambers and is a closed system. Dye

oxidation and deterioration are not an issue!

Optimized RNA Hybridization Probes

LC Sciences’ Optimized RNA Hybridization Probes are

designed with normalized Tms and experimentally

tested to ensure uniform hybridization affinity to

their microRNA targets under high stringency hybridization conditions, enhancing

both the sensitivity and specificity of the probes.

Complete Content Flexibility

All of our microarrays are made to order and synthesized to each customer’s

particular specifications. We start with the most current content from the miRBase

microRNA sequence database and then add any sequences of your choice. Validate

computational predictions, confirm sequencing data, or create totally custom tiling

arrays for discovery of novel small-RNAs.

Higher Quality Data

The superior µParaflo® platform enables on-chip synthesis ensuring high probe

quality and tight process control which produces very-low-noise signals and reveals

the true biological variations of your samples. The data obtained by these

microarrays is highly reliable and reproducible as demonstrated by a significant

number of strong publications by our customers who validated their microarray data

by qPCR, Northern Blot, or both.

Data Analysis

Full data analysis is included so that you can

immediately use information derived from the

experiment. Background subtraction and

normalization are performed. For sample comparison,

a p-value calculation is performed and a list of

differentially expressed transcripts is produced based

on a predetermined p-value threshold. The results are

organized and a summary is emailed. The complete

data set including: all images, raw data, and normalized data is saved to a CD, and

shipped via overnight carrier.

Customer Total RNA

Labeling

Customer Sequences

Chip Design

Chip Synthesis

Chip QC Hybridization

Signal Amplification

Image Acquisition

Customer Analysis Report

Data Extraction

Data Analysis

Sample QC Sanger miRBase

Comprehensive “Total RNA To Data”

Service

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microRNA Profiling Microarray Service

Clear Results

µParaflo® High Performance Microfluidic Microarray Platform

Current and Customizable Probe Content

Comprehensive - Any Species in miRBase

The most comprehensive line of standard microRNA expression profiling

microarrays.

Based on the experimentally verified microRNAs listed in the miRBase sequence

database.

(http://www.mirbase.org/)

Standard arrays are available for all individual species listed in the database as well

as groups of related species (i.e. mammals, plants, viruses).

Current - 100% Coverage of the Latest miRBase & Plant miRNA Databases

The field of microRNA is rapidly evolving and the sequence database is being updated

frequently with newly discovered sequences. Many scientists predict that thousands

more microRNAs have yet to be discovered. We are the only profiling service offering

the latest probe content and microarrays available for every organism in the miRBase

Sequence Database and the Plant MicroRNA Database. Not 90% or 95% coverage, but

100% of experimentally verified microRNA sequences are represented on all of our

arrays. The fast and flexible µParaflo® technology enables us to synthesize microarrays

when ordered.

miRBase

The miRBase sequence database is a comprehensive database of microRNA sequence

data, annotation, and predicted gene targets. It is the primary public repository for

these data. Updates to the database are released approximately every four months.

Custom Probe Content

These are not spotted arrays. Each microarray is custom synthesized when ordered.

That means we can add custom content to any of our standard microRNA microarrays

with no delay in data delivery. There is no charge for the addition of up to 100 of your

custom sequences. Furthermore, the entire contents of our arrays are completely

customizable according to the customer’s design at a very affordable price.

Add controls of customer’s choice for the detection of customer-added spiking RNA

sequences and use as customer-selected internal controls.

Add probes for the detection of siRNAs and/or other small non-coding RNAs.

microRNA Discovery / Validation

These custom arrays are very versitle. When used in combination with next-gen

sequencing and/or computational methods, they provide you with powerful tools for

microRNA discovery.

Confirm new microRNAs discovered by high-throughput sequencing / validate

sequencing results.

Validate computationally predicted microRNA sequences

Screen for new microRNA sequences by tiling along a targeted region of any

known genome.

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(713) 664-7087 1-888-528-8818 Fax (713) 664-8181 info@lcsciences.com www.lcsciences.com

microRNA qRT-PCR Expression Analysis Service

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microRNA Degradome Sequencing Service

Degradome sequencing (Degradome-Seq), also referred to as parallel analysis of RNA ends

(PARE), incorporates a modified 5′-rapid amplification of cDNA ends (RACE) method with high-

throughput next-gen sequencing to provide a comprehensive means of analyzing patterns of RNA

degradation.

Because microRNAs can cause endonucleolytic cleavage of mRNA by extensive and often perfect

complementarity to mRNAs, degradome sequencing has been used to identify microRNA cleavage

sites. Degradome sequencing has confirmed many known and revealed novel plant microRNA

targets.

Bioinformatics Package Includes: Raw sequencing data – either FASTA-A or FASTA-Q files with base-calling quality scores

LC Sciences quality filtered data reduced to mappable reads, alignment, classification, & functional annotation of all mapped reads

Identification of rRNAs, tRNAs, snoRNAs, polyN and other non-coding RNAs

Distribution of degradation fragments on selected region of genome

Identification of target mRNAs

Statistical summary of mRNA degradation sites

Identification of microRNAs from miRBase related to mRNA degradation (results will be shown in a target plot diagram)

Customer data report – includes a summary of methods and statistical analysis

Confirmed microRNA targets are presented in the form of target plots (t-plots).

Score, Type, P-value

In plants, microRNAs tend to cause cleavage of their targets at the position between nucleotides 10 and 11 of the microRNA.

Next-Gen sequencing of the 5’ ends of degraded RNA products allows identification of over-represented 5’ ends (microRNA cleavage sites).

Matching cleavage sites to known microRNA sequences links microRNAs to their targets.

miRNA corresponding to

the target cleavage site

A complete Seq-ArraySM project will result in a comprehensive

publication ready customer data report.

Sequencing Data

Raw sequencing data

Quality analysis and filtering of sequencing data to reduce to

mappable reads

Custom construction of reference database(s) for mapping -

miRBase, genome, etc

Mapping of all quality reads to custom databases

Classification of all mapped reads

Length distribution of mapped sequences

Annotation documentation of mapped sequences

Alignment of sequence variants such as isomirs

Genomic and chromosomal location of sequence clusters

Prediction of new possible miRs

Detailed explanation of microRNA analysis results and their

context

SeqArray™ custom microarray probe design

Customer data report - includes a summary and all statistics

Microarray Data

Array design and layout

Array images

Raw intensity data

Expression profiles for all samples - list of detected sequences

and relative abundance of each

Statistical cross sample analysis including multi-array

normalization, t-test, ANOVA, and/or clustering analysis

1. Send us a total RNA sample - can be from a mix of tissues, treatments, developmental stages, disease states, etc.

2. Deep sequencing is performed to generate a comprehensive atlas of all possible microRNAs for your species/system.

3. In-house developed bioinformatics tools filter the raw sequencing data, map the quality reads to reference genomes or sequence

databases if they exist, classify all mapped reads as known microRNAs, novel microRNAs, or other types of small RNAs, and predict

possible novel microRNAs from unmapped reads.

4. A custom microarray is designed based on the bioinformatics

analysis of the above results and your specific research goals.

5. Microarray expression profiling is performed on small or large

sample groups by custom synthesized SeqArrays™ based on your

unique design.

microRNA qRT-PCR Expression Analysis Service

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Seq-ArraySM Services

Seq-ArraySM provides an efficient pathway from an initial broad microRNA search to focused biological insights.

Advanced

Bioinformatics

Custom

Microarray Deep Sequencing

(713) 664-7087 1-888-528-8818 Fax (713) 664-8181 info@lcsciences.com www.lcsciences.com

miRNA corresponding to

the target cleavage site

1. Zhang G et al. (2016) Integrated analysis of mRNA-seq and

miRNA-seq in the liver of Pelteobagrus vachelli in response

to hypoxia. Sci Rep 6(1), 22907 [abstract].

2. Li H et al. (2016) Microarray and genetic analysis reveals that

csa-miR159b plays a critical role in abscisic acid-mediated

heat tolerance in grafted cucumber plants. Plant, Cell & Environ

[Epub ahead of print] [abstract].

3. Han X et al. (2016) Integration of small RNAs, degradome and

transcriptome sequencing in hyperaccumulator Sedum

alfredii uncovers a complex regulatory network and provides

insights into cadmium phytoremediation. Plant Biotech J 14(6),

1470-1483 [abstract].

4. Li X et al. (2016) Comparative Small RNA Analysis of Pollen

Development in Autotetraploid and Diploid Rice. Int J of Mol

Sci 17(4), 499 [abstract].

5. Sun S et al. (2016) Identification and comparative analysis of

the oriental river prawn (Macrobrachium nipponense)

microRNA expression profile during hypoxia using a deep

sequencing approach. Comp Biochem and Phys Part D: Genomics

and Proteomics 17,41-47 [abstract].

6. Chen J et al. (2016) Identification of miRNAs and their targets

through high-throughput sequencing and degradome

analysis in male and female Asparagus officinalis. BMC Plant

Biol 16(1), 1 [abstract].

7. Ghosh SP et al. (2016) Gamma-Tocotrienol Modulates

Radiation-Induced MicroRNA Expression in Mouse Spleen.

Rad Res 185(5), 485-495 [abstract].

The Proof is in the Publications Our microRNA discovery and analysis customers have been

publishing routinely since we became the first company to offer a

microarray expression analysis service back in 2005. Numbering over

1000 now, these studies by leading researchers in the field

contribute to a fast growing body of knowledge defining this recently

discovered class of regulatory RNAs.

Recent Customer Publications

@LCSciencesLLC @LCSciences LC Sciences LLC

www.lcsciences.com 1-888-528-8818

microRNA Discovery & Profiling Services