Servizi disponibili

The Visium Spatial Gene Expression solution by 10X Genomics enables spatial profiling of gene expression in intact tissue sections, preserving cellular spatial context. For fresh-frozen tissues, the protocol involves sectioning, mounting, fixation, permeabilization, reverse transcription, library preparation, sequencing, and spatial mapping. For FFPE tissues, additional steps include deparaffinization, rehydration, antigen retrieval, and tissue mounting with Visium Cytassist. Both protocols end with library preparation, sequencing, data analysis, and spatial mapping to retain spatial information.

Go to the open call

Total RNA sequencing comprehensively analyzes the transcriptome, revealing mRNA and non-coding RNA profiles. This technique aids in understanding gene expression, identifying novel transcripts, and deciphering regulatory mechanisms in various biological processes. The process involves RNA extraction, ribosomal RNA depletion, cDNA library generation via reverse transcription, fragmentation, adaptor ligation, PCR amplification, high-throughput sequencing, and bioinformatic analysis for gene expression quantification and transcript discovery.

Libraries are prepared using the Illumina Total RNA Prep protocol (Illumina) with Ribo-Zero Plus that supports diverse RNA inputs, including FFPE and low-quality samples, and incorporates Ribo-Zero Plus or Ribo-Zero Plus Microbiome for efficient removal of abundant RNA from various species, including human, mouse, rat, bacteria, and complex microbial samples like stool, ideal for meta-transcriptomic studies.

Go to the open call

Our service focuses on introducing INDELs (frame-shift mutations) to generate gene knock-out lines (KO), each targeting a single gene in either hPSCs or immortalized/cancer cell lines.

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.

We generate up to 3 homozygous knockout (KO) clones. Heterozygous KO clones can be provided upon agreement with the applicant. If technically feasible, clones will be analyzed for the occurrence of allelic dropout.

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

Go to the open call

Small RNA sequencing is crucial for studying short RNA molecules (18-30 nt) involved in gene regulation. It analyzes miRNAs and small RNAs, shedding light on gene regulation, development, and disease. The process involves RNA extraction, size selection, adapter ligation, library amplification, size selection, sequencing, and bioinformatics analysis to identify and quantify small RNAs. High-throughput sequencing reveals small RNA profiles, which are analyzed through bioinformatics to identify miRNAs, siRNAs, and piRNAs, aiding in understanding their roles in cellular processes.

Libraries are prepared using the SMARTer smRNA-Seq Kit (Takara) that is compatible with total RNA or enriched small RNA, incorporating SMART technology and primers with locked nucleic acids (LNAs). Users can analyze various small RNA species and create complex sequencing libraries. Illumina adapters and index sequences are added during library amplification, ensuring unbiased representation of diverse small RNA species.

Go to the open call

Single-cell multiome ATAC + Gene Expression technology by 10X Genomics enables concurrent profiling of chromatin accessibility and gene expression at the single-cell level, offering a holistic view of cellular molecular landscapes. It aids in understanding cellular diversity, identifying cell types, deciphering regulatory networks, and correlating chromatin accessibility with gene expression.

The ATAC-seq component assesses the accessibility of chromatin, offering insights into regions of the genome that are open and accessible for transcription factors and other regulatory elements. Concurrently, the RNA-seq component captures messenger RNA transcripts present in each nucleus, shedding light on active genes and their expression levels.

The workflow involves cell isolation, nuclei preparation, transposase reaction for ATAC-seq, GEM formation, reverse transcription for RNA-seq, library preparation, high-throughput sequencing, and specialized bioinformatics analysis for data processing.

Go to the open call

Single-cell immune profiling with 10x Genomics technology enables 5′ RNA sequencing at the single-cell level, alongside profiling T-cell and/or B-cell receptors at single-cell resolution by sequencing V(D)J regions. Cells are isolated into droplets, where RNA is barcoded at the 5′ end. cDNA synthesis and targeted amplification yields three types of libraries: GEX libraries for single-cell gene expression analysis, and libraries for TCR and BCR gene profiling. Pooled libraries undergo high-throughput Illumina sequencing. Bioinformatics tools demultiplex reads, assign to cells based on barcodes, and identify T and B cell clones, providing insights into gene expression and immune cell repertoire diversity and clonal expansion.

Go to the open call

Single-cell ATAC sequencing with 10X Genomics profiles chromatin accessibility of individual cells/nuclei, revealing cellular heterogeneity and regulatory processes. The scATAC-seq protocol involves cell isolation, nuclei extraction, transposase reaction for chromatin fragmentation and adapter addition, GEM formation for nuclei encapsulation with unique barcodes, library preparation via PCR amplification, high-throughput sequencing, and data analysis to identify accessible chromatin regions.

Go to the open call

Single-cell 3′ RNA sequencing with 10x Genomics technology allows gene expression study at a single-cell level, profiling thousands to tens of thousands of cells in parallel. It captures cellular heterogeneity, identifies rare cell types, and discerns gene expression differences, enhancing understanding of cellular diversity. The process involves cell isolation into droplets, RNA capture and barcoding and cDNA synthesis, library preparation, pooling, sequencing, and bioinformatic analysis for single-cell transcriptomic profiling.

The Single Cell Gene Expression Flex assay by 10X Genomics, enables single-cell/nuclei RNA-seq libraries from formaldehyde-fixed cells and tissues, including FFPE blocks. Utilizing sequence-specific probe pairs for about 18,000 human and 19,000 mouse genes, this method accounts for RNA degradation. Sample multiplexing, facilitated by sample barcodes in probes, allows pooling of discrete cell populations, accommodating up to 16 samples and potentially analyzing 128,000 cells per GEM reaction.

Go to the open call

The NF for Genomics will provide sequencing of pools of libraries prepared by the users with the NovaSeq6000 sequencing platform (Illumina).

The NovaSeq 6000 sequencing platform by Illumina offers high-throughput capabilities, making it ideal for diverse genomic studies. With its scalability and sequencing-by-synthesis technology, it efficiently generates large amounts of sequencing data. Its dual-flow cell design allows parallel sequencing of multiple samples, reducing turnaround times. Common applications include whole genome sequencing, exome sequencing, transcriptome analysis (bulk and single-cell RNA-Seq), metagenomics, epigenomics, and population genomics. This platform is pivotal for comprehensive genomic research, from understanding genetic variations to characterizing microbial communities and studying epigenetic modifications.

Go to the open call

The NF for Genomics will provide sequencing of pools of libraries prepared by the users with the NextSeq2000 sequencing platform (Illumina).

The NextSeq 2000, an Illumina platform, is renowned for its high-throughput benchtop sequencing capabilities, offering flexibility and scalability for diverse applications. It employs sequencing-by-synthesis technology, capturing emitted fluorescence to determine DNA sequences. With versatile configurations, it supports various flow cell setups and sequencing kits, catering to different project scales. Commonly used for whole genome sequencing (WGS), RNA sequencing (RNA-Seq), targeted sequencing (including amplicon sequencing and target capture), exome sequencing, metagenomics, and ChIP-Seq and epigenomics studies, the NextSeq 2000 is pivotal in genomics research, enabling comprehensive analysis of genetic and epigenetic features across diverse biological samples.

Go to the open call