SINGLE-CELL APPLICATIONS
ABOUT
When interested in cell-to-cell variation or spatial differences in expression patterns, the input quantities (or quality) drive the applications you may or may not apply.
We currently have the following applications in our portfolio :
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Single-cell RNAseq using the Takara Bio SMART-Seq v4 metholodogy
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Single-cell RNAseq using the 10x Genomics Chromium Controller and the Chromium Next GEM Single Cell 3ʹ Reagent Kits v3.1
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Single-cell ATACseq using the 10x Genomics Chromium Controller and the Chromium Single Cell ATAC Reagent Kits User Guide v2
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Single-cell Genome & Transcriptome (G&T) sequencing according to Macauley et al, 2015
We are setting up a single-cell omics core facility, with Prof. Dr. Kiavash Movahedi of the LMCT (Laboratory for Molecular & Cellular Therapy of the VUB) as technical/scientific director.
METHODOLOGY
These pages are currently under development.
Application-specific pages will appear in due time, but in the meantime do not hesitate to contact us in case of any questions.
More information on the the sequencing part (following the processing of the single cells) can be retrieved here :
INSTRUMENTS
The following devices are used for single-cell sequencing in our premises.
10x Genomics Controller
Microdroplet generator to partition single cells and to barcode RNA/DNA using the 10x Genomics Next GEM technology.
Illumina NovaSeq 6000
Our highest capacity short read sequencer. This device can generate reads up to 250 bp in length (on the SP flowcell) and generate up to 10B reads per flowcell (S4).
CERTIFICATES
Under validation
DOWNLOADS
CONTACTS
BRIGHTcore general inquires
+32 (0)2 477 64 79 (sec)
UZ Brussel
BRIGHTcore
Laarbeeklaan 101
1090 Brussels
SAMPLE TYPES
We aim to keep te list with sample types updated. However, if you believe we offer this test on other sample types, of if you have a very specific sample type you'd like to evaluate : please contact the corresponding persons for either diagnostic or research purposes.
Tissue | Recipient | Quantity | Transport | Purpose / Extract |
|---|---|---|---|---|
Cells of various tissue origins | Microtube* with cells on lysis buffer | > 5 million cells | Dry ice | RNA |
Cells of various tissue origins | Microtube* with cell pellet or on lysis buffer | > 5 million cells | Dry ice | DNA |
* Microtube can be a either a cryovial or eppendorf tube (0,5 ; 1,5 or 2 ml). Please consider the quality of the tube used (nuclease free ; free of RNA/DNA ; sterile ; LoBind) according to application needed.
DELIVERABLES
Below, you can find the type of data files that can be retrieved for this test.
If you require more information or need a more custom output, please consult our Bioinformatics page.
Deliverable | Description | Research or diagnostic |
|---|---|---|
Run folder | The complete run folder can be transferred if it concerns a run reservation (private run) | RUO (on request) |
Raw data - fast5 file | Raw data file generated by Oxford NanoPore sequencers | RUO (on request) |
Raw data - bam file | Binary data file containing the aligned reads | RUO (on request) |
Raw data - fastq file | Data file containing the raw (unaligned) reads | RUO (on request) |
PLAN EXPERIMENT
Please get clearance from your local ethical committee and/or register your samples with a biobank.
To set experiments up with us, please follow the steps below.
Get in touch
Explain your project, so we can assist you to find the best solution.
Expect questions like :
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What type of sample would you like to analyze?
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Will you handle the RNA extraction (please know : BRIGHTcore doesn't handle human pathogens)?
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In which elution buffer did you elute your RNA (we prefer nuclease free water)?
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How many samples would you like to process?
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How fast do you need the results (TAT) and/or do we need to expedite?
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If you deviate from our sample types, are there test samples available?
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Do you require bioinformatics support or are our standard deliverables ok?
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...
1
Request quotation
Once you know which experiment you want to set up, fill out the 'Quote request' form, with the essential details of your project :
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Coordinates of the person to whom to address the quotation
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Which type of test you'd like to set up
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Do you require bioinformatics support?
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Do we need to expedite (comes at extra cost)?
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...
2
Submit your samples
Once you agree with our terms (quote / TAT / terms & conditions) :
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Fill out our sample submission form
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Send it via email : contact us
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Print out the form and include it with your samples
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Send your samples to us
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Adhere to the corresponding transport conditions listed under Sample types
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Label your tubes/plates correctly : see details here
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Please attach the 'verzendinstructies' (see downloads) on the shipping container (for RNA)
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Indicate if we can discard your samples after completion of project
3
Your experiment starts
Now it is up to us... We will start your experiment as soon as possible. When expedited, we will start the experiment within 1 week. For standard requests the turn-around-time (TAT) varies :
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In diagnostics : 5 workdays
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In research : 4 weeks (or otherwise agreed)
The research TAT is generally overestimated, but this extended timeframe allows us to : combine similar requests of multiple scientists and to repeat the experiment in case of issues.
Please refrain from contacting us in case the pre-agreed TAT didn't expire yet.
