* This offer is valid until the end of 2020 or while stock lasts. The offer is eligible for all CORALL Total RNA-Seq Library Prep Kits (Cat. No. 095, 117-119, 132-134), except bundles with RiboCop rRNA Depletion Kits (Cat. No. 096, coming soon: 146, 147) and applies for direct customers only. This offer does only apply to the following countries: Austria, Germany, Switzerland, India, Australia, UK and US. Place your order at the Lexogen webstore by using the promo code CORALL-30-2020 or contact your local sales representative for a quote. This offer cannot be combined with any other Lexogen’s discounts or promotions.


CORALL Total RNA-Seq Library Prep Kit

The CORALL Total RNA-Seq Library Prep Kit enables fast and cost-efficient generation of UMI labelled, stranded libraries for whole transcriptome analyses using Illumina® NGS platforms.

Transcript Coverage

CORALL generates transcriptome-wide smooth, uniform read coverage, comparable to that of competitor kits (Fig. 1).


Figure 1 | Accumulated transcript body coverage (whole transcriptome). Coverage across all transcripts was generated using the geneBody_coverage.py tool provided by RSeQC (transcripts length normalized to 100 %).

Gene Detection

CORALL delivers excellent gene discovery rates matching conventional competitor kits (Fig. 2A). 95% of genes are commonly detected between CORALL and each of the two competitors (at >10 counts per million (CPM), Fig. 2B). This high level of library complexity ensures faithful representation of the transcriptome, enabling sensitive expression profiling.


Figure 2 | Gene detection. A) Gene discovery rates. The number of detected genes is plotted against the total number of reads mapping uniquely to exons (calculated with featureCounts). B) Overlap of detected genes. The Venn diagram illustrates overlaps between CORALL and competitor kits for genes detected with normalized expression levels >10 CPM (for uniquely mapping reads).

Superior End-to-End Coverage

CORALL’s comprehensive coverage delivers improved transcript start and end site representation. Read coverage was analyzed using the ERCC spike-in controls, which feature precise, known transcription start and end sites (TSS and TES, respectively). CORALL reads map more accurately to the exact ERCC TSS (Fig. 3A) than competitor libraries, which fail to cover the true start sites. Additionally, CORALL provides elevated coverage at TES (Fig. 3B).

Figure 3 | Normalized ERCC coverage of A) TSS and B) TES. Normalized coverage of accumulated mapped reads for all detected ERCCs. The absolute nucleotide positions relative to the TSS (red dotted line, A) and TES (blue dotted line, B) are shown.

Flexible Input

CORALL libraries can be prepared from poly(A)-enriched or rRNA-depleted RNA (100 – 200 ng of total RNA yields approximately 1 – 2 ng of rRNA-depleted RNA). We recommend using Lexogen’s RiboCop rRNA Depletion Kit V1.2 (Cat. No. 037) or Poly(A) RNA Selection Kit (Cat. No. 039). Total RNA without prior depletion or enrichment (100 pg to 100 ng) can also be used as input.

Unique Molecular Identifiers (UMIs) seamlessly included

UMIs are seamlessly introduced into CORALL libraries as an inherent part of the protocol. As a result Read 1 contains the UMI information making it directly accessible in the cost-efficient single-read mode.

Data Analysis

A Data Analysis Pipeline is now available on the BlueBee® Genomics Platform. The provided pipeline enables kit users to perform read quality control, mapping, Unique Molecular Identifier (UMI) deduplication, and transcript quantification. For using your activation code register an account with BlueBee (https://lexogen.bluebee.com/portal) and upload your data (fastq.gz files).

Enhanced Multiplexing

CORALL libraries can be multiplexed using up to 96 i7 indices (included in the single indexing kit, Cat. No. 095, 096). Additional i5 indices can also be introduced using the Lexogen i5 6 nt Dual Indexing Add-on Kits (Cat. No. 047). Used together, Lexogen’s 96 i7 and 96 i5 6 nt indices enable up to 9,216 different index combinations for sequencing.

NEW! CORALL Total RNA-Seq library prep is now also available with up to 384 pre-mixed Unique Dual Indices (Cat. No. 117, 118, 119). Lexogen’s new 12 nt UDIs featuring superior error correction for maximal sequencing data output and are also available as stand-alone Add-on Kits (Cat. No. 107 – 111) for use with other library preps. For further questions, please contact support@lexogen.com.

Fast and Easy All-in-One Protocol

The streamlined RNA fragmentation-free protocol generates ready-to-sequence libraries in 4.5 hours.


Reverse Transcription
Step 1:
CORALL Total RNA-Seq Library Prep uses total, poly(A) enriched
or rRNA depleted RNA as input.
Reverse Transcription
Step 1:
CORALL library generation is initiated by random hybridization
of Displacement Stop Primers (DSP) with partial Illumina-compatible
P7 sequences, to the RNA template. No prior RNA fragmentation is
necessary, as the insert size is determined by the distance between
hybridized DSPs. Reverse transcription extends each DSP to the next,
where transcription is effectively stopped. This stop prevents spurious
second strand synthesis, maintaining excellent strand specificity.
Linker Ligation
Step 2:
Highly efficient ligation of Linker Oligos to the 3’ ends of first-strand
cDNA fragments then introduces partial Illumina-compatible P5
sequences and Unique Molecular Identifiers (UMIs).
Library Amplification
Step 3:
During PCR, second strand synthesis is performed, and the
double-stranded cDNA is amplified. In doing so, i7 and (optional)
i5 indices as well as complete adapter sequences required for
cluster generation on Illumina instruments are added.
Step 4:
The UMI is positioned to be read out at the beginning of Read 1
during sequencing and can therefore be assessed even in Single-Read
mode. All purification steps are based on magnetic beads, rendering
the protocol highly suitable for automation.


Frequently Asked Questions

Please find a list of the most frequently asked questions below. If you cannot find the answer to your question here or want to know more about our products, please contact support@lexogen.com.

CORALL has broad species compatibility. Libraries have been successfully generated using: human (including whole blood RNA and leukocyte RNA), mouse, bacterial, plant, hamster, and mini pig RNA samples.
Any input amount between 1ng and 1 µg of total RNA for rRNA depletion or poly(A) enrichment, or up to 100 ng input for total RNA without enrichment/depletion can be used.
We do not recommend multiplexing Lexogen libraries with libraries from other vendors in the same sequencing lane.

Though this is possible in principle, specific optimization of index combinations, library pooling conditions, and loading amounts may be required, even for advanced users. Sequencing complex pools that include different library types at different lane shares may have unpredictable effects on sequencing run metrics, read quality, read outputs, and / or demultiplexing performance. Lexogen assumes no responsibility for the altered performance of Lexogen libraries sequenced in combination with external library types in the same lane (or run).

Due to size differences, libraries prepared with the Lexogen Small RNA-Seq Library Prep Kit (or any other small RNA library prep kit) should not be sequenced together with QuantSeq, QuantSeq-Flex, SENSE, or CORALL libraries. Please refer to the sequencing guidelines for each library type (library adapter details, loading amounts to use, and use of custom sequencing primers, etc), which are provided in our Library Prep Kit User Guides, and online Frequently Asked Questions (FAQs).

CORALL libraries can be sequenced either with single-read (SR) or paired-end (PE) sequencing. We can recommend SR50 – 200, or PE100 – 150. The choice of sequencing format may also depend on the particular application.

Please follow loading amount recommendations provided by Ilumina for your specific instrument, or contact info@lexogen.com for further information.

CORALL libraries can be analyzed using most standard RNA-Seq pipelines. The ideal workflow may depend on the goal of the sequencing experiment. Further information on recommendations for trimming, quality control, and alignment of CORALL reads can be found in the Data Analysis section of the CORALL product page, or in the CORALL User Guide, Appendix H, p.34.

A pipeline is available on the BlueBee® Genomics Platform that performs read quality control, mapping, Unique Molecular Identifier (UMI) deduplication, and transcript quantification.
Figure 1 | CORALL Data Analysis Pipeline Workflow.

Activation codes for data analysis can be purchased via the web shop. Each code enables 24 data analysis runs (i.e., 24 Fastq.gz files may be analyzed). Reference genomes for various species are available (please contact support@lexogen.com for more information).

For using your activation code register an account with BlueBee (https://lexogen.bluebee.com/portal) and upload your data (fastq.gz files) to a new project. To execute runs, navigate to your project and go to runs -> add run select the data you wish to analyze and the species from the dropdown list then click run.

The qPCR assay is recommended to set the optimal number of PCR cycles for the library amplification. This will avoid under or overcycling. Undercycling may result in insufficient library for sequencing, and overcycling can lead to higher duplication levels and quantification biases.

To perform the qPCR assay please ensure you purchase these additional reagents along with your CORALL Total RNA-Seq Library Prep Kit:

  • PCR Add-on Kit for Illumina (Cat. No. 020.96) – Available from Lexogen
  • SYBR Green I Nucleic Acid Stain (10,000x in DMSO) – Available from Sigma- (Cat. No. S9430) or ThermoFisher (Cat. No. S7585).

NOTE! The use of SYBR Green-containing qPCR Mastermixes is explicitly NOT recommended. The SYBR concentrations may be inhibitory, or the buffer/enzymes included may alter the qPCR efficiency. This may lead to inhibition of amplification in general, or inaccurate endpoint cycle number calculations.

Please note that the use of EvaGreen dye at final concentrations of 0.1x – 1x is not officially recommended, as it is not fully compatible with the specified qPCR assay for cycle number calculation. Amplification curves generated using EvaGreen may be delayed and show reduced maximal fluorescence intensity compared to SYBR Green I dye. Therefore, endpoint cycle numbers may need to be calculated differently and verified by Endpoint PCR testing.

The qPCR is particularly important for FFPE and low or variable quality RNA input samples, and low RNA input amounts. Please be aware that different sample types (species, tissues, cell types), or the use of different upstream RNA processing steps (i.e. enrichment and selection methods) may affect the mRNA or non rRNA content of the sample. Therefore, more or less PCR cycles may be required, even if input amounts between sample types are consistent.

Yes, low quality and FFPE samples can be used with CORALL. Protocol modifications are recommended for library preparation from degraded RNA and FFPE samples with CORALL library prep kit. The following recommendations have been evaluated with 25 – 500 ng total RNA input:

  • Perform DNase I treatment prior to rRNA depletion (without an intermediate cleanup step).
  • In step 32 use 36 µl of PB (instead of 27 µl) for single indexing, or 42 µl of PB (instead of 31.5 µl) for dual indexing.
  • Optional: Add SIRV-Set 3 (0.1 – 0.2 % of target RNA fraction) prior to DNase I treatment.

Sequencing is recommended with SR75.

For further questions, please contact support@lexogen.com.

The Lexogen i5 6 nt Dual Indexing Add-on Kits contain the indexed i5 adapters only. They can be used to introduce dual indexing for all Lexogen library prep kits that include the Lexogen i7 6 nt Indices (015, 016, 095, 001). The indices of the i7 and i5 6 nt Index Sets are 6 nucleotides long. The Lexogen UDI 12 nt Unique Dual Indexing Kits contain pre-mixed i5 and i7 adapters, each 12 nucleotides long.

When using the UDI 12 nt Sets for introduction of Unique Dual Indexing to libraries prepared with Lexogen kits that include the Lexogen i7 6 nt Indices (015, 016, 095, 001), the PCR (yellow) from the library prep kits has to be replaced by the Dual PCR Mix (purple) from the UDI 12 nt Add-on kits and the 12 nt UDIs are used instead of the i7 6 nt indices.

For convenience the QuantSeq FWD and CORALL kits are available as versions containing the UDI 12 nt Sets instead of the i7 6 nt Index Sets (113-115 and 117-119, respectively).

For more information on Lexogen Unique Dual Indexing solutions please visit www.lexogen.com/indexing/12nt-dual-indexing-kits/.

Lexogen UDI 12 nt Unique Dual Indexing Add-on Kits are compatible with QuantSeq FWD and REV (Cat. No. 015, 016), QuantSeq-Flex (Cat. No. 033, 034, 035), CORALL (Cat. No. 095, 096) and SENSE mRNA V2 (Cat. No. 001) Library prep kits.

The Lexogen UDI 12 nt Unique Dual Indexing Sets are not compatible with Small RNA library preparation kit (Cat. No. 052).


CORALL Total RNA-Seq Library Prep Kit for Illumina

pdf User Guide – update 31.03.2020
pdf User Guide – CORALL Total RNA-Seq Integrated Data Analysis Pipelines on BlueBee® Genomics Platform – release 20.07.2020
pdf Product Flyer – update 20.09.2019
pdf PCR Add-on Kit for Illumina Instruction Manual – update 03.07.2019
pdf i5 Dual Indexing Add-on Kits (5001-5096) Instruction Manual – update 12.03.2019

pdf Lexogen i7 and i5 Index Sequences – update 05.05.2020
pdf Library Quantification Calculation File

Material Safety Datasheets

MSDS Information can be found in the Documents page.

If you need more information about our products, please contact us through support@lexogen.com or directly under +43 1 345 1212-41.

CORALL Free Trial Kit

Dear Customer,

If you would like to receive a CORALL Total RNA-Seq Free Trial Kit, please fill in the form.

If you have any questions, please do not hesitate to contact us at info@lexogen.com or +43 (0) 1 345 1212 – 41.

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