Illumina MiSeq Sample Submission Form
Project number (filled by FMSC)
Project title (with one sentence)
Project Description
CONTACT INFORMATION
Contact person(s)
 Name(s)
 Email(s)
 Address
 Phone
Group leader/Principal investigator
 Name
 Email
 Address
 Phone
Biocity Turku Research Programme
(must be filled by Biocity Turku groups)
INVOICING INFORMATION
Internal invoice
(University of Turku account)
 Name
 Department/Laboratory
 Cost pool (kustannuspaikka)
 TY project code: 26xxxxx
External invoice
(other than University of Turku account)
 Institution
 Department/Laboratory
 Address
 Cost pool (kustannuspaikka), if
applicable
 VAT number
PROJECT OPENING MEETING


Date
Participants (FMSC + customer)
MiSeq Sample Submission Form 2014
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MiSeq PROTOCOL INFORMATION
Read length
Analysis application type
Number of lanes
x 50 bp
x 75 bp
x 150 bp
x 250 bp
x 300 bp
Targeted RNA-seq
Targeted DNA-seq
Custom Amplicon -seq
Metagenomics (16S-seq)
Small genome re-sequencing
smallRNA-seq
Clone-seq
Other: ______________________
No. of runs used in sequencing:
No. of samples per run:
Additional library preparation protocol
information (e.g. special kit)
SAMPLE INFORMATION
Total number of samples
(including biological replicates)
Organism
Sample type
 Tissue, origin
 Cells, origin
 Blood, origin
 Other, what
Sample material
 gDNA
 totalRNA
poly(A) RNA
smallRNA
PCR Amplicon
ready MiSeq library
Other:_______________________
DNA / RNA extraction method

Other possible pre-processing done to 
the samples
(please specify all applied protocols)
MiSeq Sample Submission Form 2014
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SAMPLE LIST
Avoid spaces and any special characters in the sample names. Please use group names
and sample names that will allow an easy interpretation of the name coding during data
analysis. (Add rows if needed.) Also check the prices with FMSC if your total sample
number has changed.
Sample
Sample
name
Sample
group
c, ng/l
A260/A280
Volume,
l
Comments
Index
Pooling
group
1
2
3
4
5
6
7
8
9
10
11
12
13
14
15
GROUP DESCRIPTIONS
Please give a short description of each sample group (add rows if needed). Please note
that if you have changed your original sample setup from the one discussed with our
bioinformaticians, you should contact them (bioinfo@btk.fi) to discuss the changes
before continuing further. This concerns especially those projects where the data
analysis service is used.
Sample group
Num. of biological
replicates
Description
COMPARISON TO A SET OF PREVIOUS OR FUTURE RESULTS
If you are planning to compare these results with a previous set of
results produced using our service, please indicate here the time
when the previous samples were processed
If you are planning to compare these results directly with a
possible future set of samples that will be processed using our
service, please indicate this here and also give us some estimate
when these samples will be processed. (It should be noted that after
longer time the same equipment and protocols may not be available anymore,
complicating the integration between earlier and later data set)
MiSeq Sample Submission Form 2014
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DATA ANALYSIS SERVICE

I would like to purchase the full bioinformatics data analysis service (please
contact the bioinformatics team for pricing and details bioinfo@btk.fi)

Data will be analyzed through collaboration with the FMSC
bioinformatics group (as agreed previously)

I will analyze the data myself, data will be sent to this e-mail address:
FILL IN DIRECT COMPARISONS BETWEEN GROUPS
if FMSC's bioinformatics team will analyze the data
Use group names given in the sample information table. Remember that all groups do
not necessarily need to be directly compared but the lists of differentially expressed
genes between several independent comparisons (e.g. for different tissues) can also be
compared.
Comparison Comparison group
0 (example)
KO (knock-out group)
Baseline group
WT (wild type group)
1
2
3
4
5
6
7
8
9
10
Paired samples
Please indicate clearly (by e.g. sample
naming) the samples that originate from the
same biological individual as this information
is needed in the analysis.
Other information for the bioinformatic
analysis (e.g. other factors linking certain
samples together like handling day etc.)
MiSeq Sample Submission Form 2014
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COLLABORATION WITH FMSC
This page is to be filled by only those with whom collaboration has previously been
agreed.
Type of collaboration
 Lab
 Bioinformatics
Financing of the project
(What does each group contribute to
material and personnel, given as detailed
as possible, if relevant include payment
schedule)
FMSC members to be included as
coauthors to publication(s)
Other issues
(e.g. Secrecy, place for storage of samples,
time plan for discarding remains of
samples, use of remaining samples for
other purposes than this project.)
MiSeq Sample Submission Form 2014
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Sample submission requirements and service work agreement
The sample requirements and sample preparation instructions are described below for the different types
of samples. FMSC will always check the quality of the samples (or libraries) prior to sequencing and the
customer is contacted if there is a concern related to sample quality. Please note that samples can be
processed with customers consent even in the case they do not meet the quality requirements but in these
cases FMCS will not be able to guarantee successful sequencing results. Please do not hesitate to contact
ngs@btk.fi for any further questions.
Ready-made libraries for sequencing

All library concentrations and fragment profiles should be similar in the same sample set.

If several libraries are pooled in one run, it is important to maintain color balance for each base of the
index read for optimal de-multiplexing. FMSC personnel can assist in the selection of color balanced
indexes before library preparation.

Individual libraries prepared by the customer for pooling and MiSeq sequencing should be delivered in at
least 4nM concentration and 10 µl volume. If the customer wants to pool his/her individual libraries
themselves, the results of the concentration and size distribution measurement as well pipetting charts for
pooling should be provided.

Pooled and normalized libraries prepared with Nextera XT or TruSeq Custom Amplicon kits should be
provided with a minimum volume of 25µl.
RNA samples for library preparation and sequencing

Samples are recommended to be delivered as total RNA in order to ensure purity and quality of the starting
material before library preparation.

It is recommended that only the required amount of RNA is sent since FMSC does not have extra storage
space reserved for sample storage.

All samples in the same set should be of equal purity and quality. The absorbance ratio A260/A280 for
pure RNA is 2.0-2.2 and the integrity number(RIN) for intact total RNA above 8.0

Total RNA should be provided in 200 ng/µl and minimum volume of 10 µl.

RNA that has DNA contamination will result in underestimation of the amount of RNA used. To prevent
this, DNase step is recommended, but not required being included with the RNA isolation method.

If RNA material meeting the criteria can’t be provided due to special circumstances such availability
source material for RNA extraction alternative workflows for these cases exist and the possibilities should
be discussed separately.
DNA samples for library preparation and sequencing

Samples are recommended to be delivered as genomic DNA in order to ensure purity and quality of the
starting material before library preparation.

It is recommended that only the required amount of DNA is sent since FMSC does not have extra storage
space reserved for sample storage.

All samples in the same set should be of equal purity and high quality. The absorbance ratio A260/A280
for pure DNA is 1.8-2.0.

Genomic DNA samples should be diluted to 200 ng/ul concentration and in minimum volume of 10µl.

DNA should be quantified using fluorescence based method such as Picogreen or Qubit.

RNA contamination results in underestimation of the amount of DNA used. Therefore RNase step is
recommended but not required to be included with the DNA isolation method.

If PCR products are provided the estimated length of the products should be provided.

If DNA material meeting the criteria can’t be provided due to special circumstances such availability
source material for RNA extraction alternative workflows for these cases exist and the possibilities should
be discussed separately.
MiSeq sequencing run and result delivery

The typical yield for a MiSeq run is 20-50 x 106 paired-end reads, depending on the version of sequencing
reagents used. Sequencing will be rerun without extra costs in case of technical failure during the
sequencing if it is not related to the nature or quality of the libraries.

The raw data in Illumina’s default format (fastq) will be downloadable within a week after the sequencing
has been finished.
Sample and data storage

FMSC will discard the left over RNA/DNA sample material after 1 year. Please deliver only the amount
of sample needed for the analysis.

If extra material is for some reason sent and customer wishes to have it returned, it has to be agreed
separately. Customer has to cover the possible costs related to the returning of the sample material.

FMSC will store data only for a short time and the customer is responsible for storing the raw data after the
project is finished and the data has been delivered to the customer.
MiSeq Sample Submission Form 2014
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Send us this sample submission form both in print with your samples and
electronically as an e-mail attachment to ngs@btk.fi. We require a signed copy of
this document prior to processing the samples. Please check detailed sample submission
instructions on our website at http://fmsc.btk.fi.
As Principal Investigator on this project, I agree to:
1. Acknowledge the use of the Finnish Microarray and Sequencing Centre's
analysis service in the materials and methods section in any resulting
publications.
2. Send a reprint of each resulting publication to the Finnish Microarray and
Sequencing Centre.
3. Include all involved FMSC members (see previous page) to my resulting
publication(s) (where the analysis results are used) as coauthors if collaboration
has been agreed with them. I will also send the manuscript for their review prior
to submitting to a journal.
_______________________
Date
MiSeq Sample Submission Form 2014
_______________________
Signature
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