Project submission#

Please submit your sequencing and single cell project online using Calpendo

Sequencing projects#

Sample requirements#

DNA/HMW-DNA#

1. same extraction protocol

2. RNase Treatment

3. OD260/280: 1.8, OD 260/230: between 1.8 and 2.0

4. Solvent: nuclease free water or low TE (10mM Tris, 0.1 mM EDTA)

5. provide >10µl of sample

6. minimum amount:

   ⁃ ChIP DNA: 10ng

   ⁃ genomic DNA:

   • shotgun/WGS: 500ng (without PCR amplificaiton) and 50ng (with PCR amplification)

   • amplicon sequencing (16S/18S/ITS): 50ng

   ⁃ High molecular weight DNA: 5-15µg (please provide gel image)

7. use 1.5ml leak-lock tubes (from Eppendorf or similar), for 16S/18S sequencing, in PCR plate.

8. For sample submission in Calpendo nanodrop conc., 280/260 and 230/260 ratios information is mandatory

RNA#

1. same extraction protocol
2. DNase Treatment
3. OD260/280: 2, OD 260/230: between 1.8 and 2.0
4. RIN value >7 or equavilant
5. high/low MW rRNA ration ~2
6. Solvent: nuclease free water
7. provide >10µl of sample
8. minimum amount: 1µg
9. use 1.5ml leak-lock tubes (from Eppendorf or similar)
10. For sample submission in Calpendo nanodrop conc., 280/260 and 230/260 ratios information is mandatory.

Note: All our protocols use totalRNA as starting material. In case you have mRNA, rRNA depleted RNA or smRNA please check with us before to confirm the compatability with the protocol.

Prepared Library#

1. Minimum concentration: 10nM
2. Volume: >10µl
3. Bioanalyzer report for individual libraries
4. use 1.5ml leak-lock tubes (from Eppendorf or similar) or PCR plate

Samples not fulfilling the sample requirements will FAIL at the sample QC step and will not be processed further.

Sample Labelling#

DNA/ HMW-DNA#

1. Unique name
2. Sample name can only have alphanumeric (a-z, 0-9), dash (-) and underscore (_) values.
3. Date
4. Submitter name
5. Sample concentration

RNA#

1. Unique name
2. Sample name can only have alphanumeric (a-z, 0-9), dash (-) and underscore (_) values.
3. Date
4. Submitter name
5. Sample concentration

Prepared Library#

1. Unique name
2. Sample name can only have alphanumeric (a-z, 0-9), dash (-) and underscore (_) values.
3. Date
4. Submitter name
5. Sample concentration

Online sample submission#

The general terms and conditions for platform services can be downloaded from here.

Before sample submission to the platform, sequencing project and sample information need to be submitted online at Calpendo.

You will be asked to provide an OTP in the billing/invoicing tab at the time of project creation. Please discuss with your PI which budget code to use. This will be used for internal invoicing after completion of the project. For external users the Purchase Order (PO) number need to be provided in the tab. Please send the soft copy of PO to LCSB-sequencing@uni.lu before sending samples for sequencing. The sample processing will start with the reception of the PO.

For more than one sample submission CSV (comma separated) file can be used. Template csv file can be downloaded for the DNA, RNA and Library or from Calpendo.

Sample delivery#

Please drop your samples in a dedicated tray in delivery freezer at BT1 room 501. The samples will be picked from the tray on Tuesday/Thursday after 16:00hrs. Incorrectly labelled boxes/samples will not be picked and might lead to unnecessary delays in the sample processing. Internal users who do not have access to BT1 building or room 501 can borrow the genomics platform access card from the guard present at the reception and return after dropping the sample box. External users (with in Luxembourg) can come for sample delivery on a prefixed date and time. For sample delivery via the post we suggest to post the package on Monday/Tuesday to minimize the risk of sample loss.

Single-cell projects#

After the kick-off meeting the online samples submission is done using via Calpendo. For single cell sample processing is scheduled for pre-agreed date and time. The samples can only be process if the project is approved for the desired date and time. The facility will check the sample quality and might decide not to process the samples if the samples quality is not satisfactory. It is possible to process such samples if PI provides the written (via email) agreement to accept the risk and cover the costs.

Sequencing Data transfer#

Internal users with HPC access: Once the sequencing run is completed, the sequencing data is available to the University of Luxembourg researchers with the access to the internal computational resources via a folder sharing (group folder on Isilon)

External users/ users with no HPC access, we offer data transfer via (i) secured FTP link, or (ii) secured folder accessibility or (iii) user provided solution -like user OneDrive, ownCloud etc. For human samples encrypted data is shared using the asperaWEB (IBM) Server.

Invoicing#

For internal users, the invoicing will be done via simple fund transfer request to SFC upon PIs approval. This invoicing is done quarterly. For external users, the final invoice for our services will be send electronically (via PEPPOL).