Single Cell Core Facility of Flemingsberg Campus (SICOF)

Welcome to The SICOF Web Portal                        

On this page, you will find the latest information on SICOF

Link to our manual for SICOF interaction: Click here 

Latest news

2021-03-25: New abbreviation and other news

 

Dear users,

In this news post, we would like to update you on a few changes in at the single cell core

  • In order to better reflect our location and goals, we have changed our acronym to SICOF: Single cell Core faciltity of Flemingsberg campus. We are now in the process of changing the naming on all documents and web pages, so for a while you might see ScCore and SICOF being used intermixed. 
  • The cost for running a Fragment Analyzer QC have been increased. Now that we are using the machine more regularly we have a better overview on the costs associated with this QC, and we had to unfortunately increase the price. The cost/sample is still very economical as compared to running a BioAnalyzer.
  • We are also glad to announce the acquisition of a new instrument to our core: The iDot liquid dispenser. This will increase the variety in liquid dispensing robots in our laboratory and will allow us to increase the throughput. 
  • Smart-seq3 implementation is proceeding well, we are now finalizing the last analysis parts and will hopefully soon be able to implement this as a stable service.
  • We have now also changed the way we classify plates according to the quality. The manual has been updated accordingly and will be available from the link on top of this page from Monday next week.
  • Please note that we have changed the phone number on our shipping address. Please use the provided landline phone number when sending packages to us.

Best regards,

SICOF

 

2021-02-17: Launch date confirmed!

 

Dear users,

We are very happy to announce that we are opening our core facility next Monday, February 22nd. We will start accepting and running projects on a first-come first-serve basis . Please also take a look at our manual linked on the top of this page. It contains important information on your interaction with our Core.

Please consider that, at the moment, we can't offer Smart-seq3 yet due to the problems described below.

With our best regards,

ScCore

 

2021-02-12: Delay on Smart-seq3 implementation + Drug-seq pricing.

 

Dear all,

 

We have discovered a potential issue with the Smart-seq3 protocol, where we are noticing a strong increase in background detection. We are now investigating the source and implications of this background. This could be due to the increased sensitivity of Smart-seq3 over Smart-seq2, but we want to rule out any problems from the SICOF side. We always strive to provide our customers with the highest data quality. Link to an illustration of the problem

On a more positive note, we have now updated our pricing on Drug-seq and can now offer this as a service. Also be aware that Drug-seq does not imply that it can only be used for drug screening. We can run the Smart-seq protocol on many samples, including cells, RNA, cDNA,... . The advantage of Drug-seq lies in the fact that many samples can be run simultaneously at a fraction of the cost of running each library separately.

Our beta-testing of iLab goes well and next week we will announce the opening date for the facility.

 

Enjoy your weekend!

 

ScCore

 

 

2021-01-22: Preparing for liftoff

Dear all,

 

First of all, we would like to wish you all a splendid 2021! May it be different as compared to 2020... For us the year started great, we are very enthousiastic to start working as a Core facility for KI!

On this page, we'll update you on the status of the SICOF on a regular basis. So, without further delay, we hereby present our roadmap for the future:

  • We have now completed our move to NEO and are settled in our new lab space. All our equipment has been serviced and the protocols are working.
  • From next week Monday, we will start using iLab exclusively for project/sample submissions. All current users will receive an email within the next hours with the SICOF manual, where our pipeline of work is explained. If you have any questions, pleae mail us at singlecellseq@ki.se
  • In a couple of weeks from now, the SICOF will open up for researchers from KI. The reason for not launching right now is that we need a few weeks to get used to iLab and the interaction with our user base, so that we can provide the best possible service to you. We will communicate the launch on this website one week in advance. Remember, we work on a first-come, first-serve basis. 
  • We are currently analyzing the costs associated with Drug-seq. After this, the prices will be updated on iLab
  • Smart-seq3 is now rigourourly being tested for reproducibility and stability, so that we can offer you excellent data from this new and exciting chemistry. Once this is done (preliminary outlook is spring 2021 but maybe earlier), we will update the pricing and offer it as a service to you.
  • From next week, we are excited to offer you new possibilities for QC. With the aquisition of an Agilent Fragment analyzer, we can now increase the number of samples to be QC'ed substantially. This is an often requested service which will allow for a better estimation of sample quality before tagmentation and sequencing. 
  • Our final goal is to be able to provide our customers with meaningful single cell data which can be browsed and explored without the need for a bioinformatician. Development of this new pipeline is progressing well and should be available soon. When this is done, a tutorial will be provided for this data exploration.
  • We are trying to exchange some expensive enzymes in the Smart-seq2 protocol for inexpensive ones, which could lead to a reduced cost in the future. More info on that coming soon!

 

And this concludes the first news post of the ScCore!

 

With our best regards,

 

ScCore.  

About us

In 2021, the Single cell core facility for Flemingsberg campus (SICOF) was established as a new, state of the art core facility to support the Karolinska Institutet South Campus research community. Our goal is to facilitate the use of single cell/nuclei sequencing technologies for all researchers. We offer several pipelines for single cell analysis, ranging from small scale ultra-sensitive solutions like Smart-seq2/3 sequencing up to larger scale droplet-based sequencing. For the latter, we use the solutions provided by 10x Genomics and can thus provide assistance with all of 10x Genomics’ products, including single nuclei ATAC-seq and the newly released Single Cell Multiome ATAC + Gene Expression assay. In addition to that, we also provide the opportunity to use our pipelines for drug screening experiments (Drug-seq) and other custom solutions. We aim to provide all researchers with clustered data that can be interpreted and analyzed without the need for a bioinformatician.

We are a team of six members: One administrator, one bioinformatician, three research engineers and one head of facility. Our laboratory is equipped with high-precision dispensers/handlers, such as an Agilent Bravo, a Labcyte Echo 525 and several smaller-scale dispensers. For QC of single cell libraries, we have three Agilent Bioanalyzers and an Agilent Fragment Analyzer. We perform our sequencing on our own Illumina HiSeq3000, which is also available for customers to run their own libraries.

 

Location and hours of operation

Hours

Location

Monday - Friday

9:00AM - 16:00PM           

NEO, Blickagången 16

Floor 7, elevator S

SE-141 57 Huddinge, Sweden

 

Shipping address

OBS: Do not ship samples to us without filling in a sample submission request!

Single Cell Core (SICOF) Room 7333
Karolinska Institutet | Institutionen för Medicin Huddinge
Hälsovägen 7C
Neo, plan 8
141 57 Huddinge
Tel 46 (0)8 52 48 34 18

E-mail: singlecellseq@ki.se 

Contacts

Name Role Phone Email Location
Single Cell Core (SICOF) mailbox

 
0706579511
 
singlecellseq@ki.se
 
Room 7333, NEO, floor 7, elevator M1
 
Michael Vanlandewijck
Head of Facility
 

 
michael.vanlandewijck@ki.se
 
NEO, floor 7, elevator S