Available Services

Direct RNA Sequencing with Nanopore technology sequences RNA molecules without cDNA conversion, offering real-time detection of RNA sequences and modifications. It preserves RNA’s native state, revealing insights into RNA processing and modifications. RNA extraction, adapter ligation, sequencing, and data analysis are key steps. Raw signals are base-called for RNA sequence reconstruction. This method can offer a comprehensive view of the transcriptome.

The Direct RNA Sequencing Kit (SQK-RNA004) facilitates native RNA sequencing, avoiding cDNA conversion. It supports poly(A)-tailed RNA or total RNA like eukaryotic mRNA and viral RNA. This upgrade enhances sequencing output and accuracy on the latest RNA flow cells (FLO-MIN004RA and FLO-PRO004RA). It includes reformulated priming reagents for flow cell compatibility and features fuel fix technology for extended experiment runs without additional fuel.

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Cell-free DNA (cfDNA) sequencing with Nanopore technology allows direct interrogation of genetic information in circulating DNA without PCR amplification. This real-time protocol enables methylation status analysis. It offers insights into cfDNA’s genomic landscape, benefiting clinical diagnostics like cancer detection, treatment monitoring, and minimal residual disease identification. The protocol involves cfDNA extraction, library preparation, loading onto a Nanopore sequencing device, real-time sequencing, and data analysis for variant calling, copy number and methylation status analysis.

The library preparation involves repairing DNA ends, dA-tailing, and ligating sequencing adapters. The kit ensures high sequencing accuracies (Q20+) on nanopore Flowcells R10.4.1, with updates for enhanced DNA capture and fuel fix technology for longer runs. The protocol is optimized for short DNA fragments recovery, based on a modified long-reads protocol.

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Nanopore cDNA sequencing allows the exploration of gene expression dynamics, alternative splicing, and RNA biology with long-read capabilities. The process involves RNA extraction, cDNA synthesis, library preparation with unique barcodes, loading onto a nanopore sequencer, real-time sequencing of cDNA strands, base calling, and subsequent bioinformatics analysis for aligning reads, identifying gene isoforms, and quantifying gene expression.

The libraries are prepared with the PCR-cDNA Sequencing Kit that enables nanopore sequencing of cDNA from low input poly(A)+ RNA or total RNA with additional optimization. It employs a strand-switching method to select full-length transcripts and incorporates unique molecular identifiers (UMIs). The kit includes the Rapid Adapter T (RAP T) for enhanced capture and fuel fix technology for longer experiments without fuel addition. A new cDNA RT adapter and RT primer reduce overlaps during reverse transcription and allow measurement of polyA+ tail lengths.

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mRNA sequencing analyzes the transcriptome, revealing gene expression patterns and novel transcripts in cells or tissues. The process involves RNA isolation, cDNA synthesis via reverse transcription, library preparation with added adapters, high-throughput sequencing, and bioinformatic analysis mapping reads to a reference genome or transcriptome to discern gene expression levels and novel transcripts.

mRNA sequencing from standard RNA input is performed with Illumina Stranded mRNA Prep protocol (Illumina) that ensures precise strand orientation measurement, uniform coverage, and high-confidence detection of novel features like isoforms and gene fusions.

mRNA sequencing from RNA low input is performed with the SMART-Seq v4 PLUS Kit (Takara). SMART technology ensures full-length transcript information, enabling analysis of isoforms, gene fusions, and mutations, with improved gene detection via locked nucleic acid (LNA) technology. High reproducibility and accurate coverage of GC-rich transcripts are ensured.

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The Biophysics Unit is equipped with instruments designed to determine the strength and biophysical properties of macromolecular or protein-ligand interactions, including association and dissociation constants, as well as stoichiometry of binding. Available techniques include isothermal titration calorimetry, microscale thermophoresis, and bio-layer interferometry (which can also be utilized for quantifying known components in complex mixtures).

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The services we provide include, but are not necessarily limited to, the following use-cases:

• • Image restoration and denoising: Removing pixel-independent noise from images to increase SNR.
  • Semantic and Instance segmentation: Identifying and segmenting objects in an image, generating image masks.
  • Quantitative Image Analysis: Quantification of intensity levels in images or segmented objects.
  • Morphometric Analysis: Analysis of shape and morphology of segmented objects
  • Custom pipeline development: Construction of an analysis pipeline combining two or more individual steps.

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Motorized, inverted wide-field microscope with digital clearing. Epifluorecence illuminator with 8 single LEDs (395 nm, 438 nm, 475 nm, 551 nm, 555 nm, 575 nm, 635 nm and 730 nm) and sCMOS camera.

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Confocal microscope with STED module and tandem scanners (conventional and resonant), white laser (up to 8 simultaneous laser lines between 440 nm and 790nm), 405 nm laser, AOBS tunable dichroic and integrated FLIM module.

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Point-scanning confocal microscope with white light laser (up to 8 simultaneous laser lines between 440 nm and 790nm), 405 nm laser, AOBS tunable dichroic, dual scanner (conventional and resonant) and integrated FLIM module.

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If the cell is supplied with a donor DNA template, Cas9-induced DSBs can be repaired by integrating DNA sequences of various lengths using homology directed repair (HDR) mechanism. We provide Knock-In (KI) services to obtain reporter cell lines (including safe harbor integrations), edited cells harboring specific single nucleotide corrections as well as labelled proteins (e.g., with fluorescence or a protein tag).

Characterization of each engineered cell line includes:

• Cell identity confirmation using STR analysis
• Confirmation of desired editing via Sanger sequencing.

• Karyotyping (Q-banding) and identification of Copy Number Variations (CNVs) at high resolution
• Master bank post-thaw viability and mycoplasma testing.
• Optional evaluation of undifferentiated stem cell markers and pluripotency markers upon 3-germ layer differentiation assay.

We accept cell lines in a cryopreserved state, with a minimum of 1 x 10^6 cells per cryovial.

The service typically requires 2 to 4 months for completion and includes the delivery of 1-3 clones, each provided in 10 cryopreserved vials.

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