Illumina HiSeq 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
The laboratory part of the project will be invoiced after the raw data delivery.
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)
HiSeq Sample Submission Form 2015
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HiSeq PROTOCOL INFORMATION
Read length
Application type
Number of lanes
 x 50 bp
 x 100 bp
 x 150 bp
stranded mRNA-seq
stranded total RNA-seq
miRNA-seq
smallRNA-seq
ChIP-seq
RRBS
Bisulfite sequencing
Targeted DNA-seq
de novo genome sequencing
genome resequencing
No. of lanes used in sequencing:
No. of samples per lane:
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
 DNA
 totalRNA
poly(A) RNA
smallRNA
ready HiSeq library
DNA / RNA extraction method


Other possible pre-processing done to 
the samples

(please specify all applied protocols)

HiSeq Sample Submission Form 2015
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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)
HiSeq Sample Submission Form 2015
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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). For service projects the bioinformatics cost will
be invoiced after the results and the analysis report have been delivered. For
collaboration projects at least 50% of the bioinformatics cost will be invoiced
after the quality and the preliminary results have been delivered and the rest
when the main results have been delivered or as agreed but latest within one
year.

I will analyze the data myself
GENERAL OBJECTIVE OF DATA ANALYSIS

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
HiSeq Sample Submission Form 2015
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is needed in the analysis.
Other information for the bioinformatic
analysis (e.g. other factors linking certain
samples together like handling day etc.)
HiSeq Sample Submission Form 2015
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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.)
HiSeq Sample Submission Form 2015
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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 may be
processed even in the case they do not meet the quality requirements but then FMCS will not be able to
guarantee the successful sequencing. Please do not hesitate to contact ngs@btk.fi for any further
questions.
Sending ready-made libraries for sequencing

Ready-made libraries for HiSeq 2500 sequencing provided by user should have a concentration of at least
2 nM. The concentration of ready-made libraries should be 1-40 ng/µl in minimum of 10 µl volume.

Library fragments should have compatible size distribution with selected read lenght in the range of 200700 bp and average fragment size should be 250-350 bp (for smallRNA libraries 120-170 bp) or according
library preparation protocol’s recommendations.

All library concentrations and fragment profiles should be similar in the same sample set.

If several libraries are pooled in one lane, it is important to maintain color balance for each base of the
index read being sequenced and thus select a set of compatible index sequences.
Sending total RNA samples for library preparation and sequencing

For RNAseq libraries total RNA samples should be diluted to 50-100 ng/µl, all in same concentration and
minimum volume of 10 ul. At least 0.5 µg, preferably 1.0 µg, total RNA is required.

For smallRNAseq libraries total RNA samples should be diluted to 200 ng/µl, all in same concentration
and minimum volume of 10 µl. At least 1.5 µg, preferably 2.0 µg, total RNA is required.

For good quality total RNA samples, the Agilent Bioanalyzer RIN value should be > 8.0 and all samples
should have similar quality.

Total RNA should be intact and pure. Using low quality or degraded RNA is not recommended with
standard protocol as the use of degraded RNA can result in low yield, over-representation of the 3' ends of
the RNA molecules, or failure of the protocol.

RNA that has DNA contamination will result in underestimation of the amount of RNA used. To prevent
this, DNase step is recommended, however, not required to be included with the RNA isolation method.

If good quality material is not available, alternative workflows exist and can be discussed separately.

When using low quality total RNA samples (RIN value < 7.0) for library preparation, all samples should
be similar and equally degraded. Only fragments above 150 bp can be used for library preparation. FMSC
does not guarantee results for samples with low RNA quality.
Sending genomic DNA samples for library preparation and sequencing

For DNAseq libraries genomic DNA samples should be diluted to 20-500 ng/ul, all in same concentration.
Minimum of 0.5-3.0 µg genomic DNA is required, depending on the library preparation protocol.

The ratio of absorbance at 260 nm to absorbance at 280 nm with values of 1.8–2.0 are considered
indicative of pure DNA.

Genomic DNA should be intact and pure, sample should be free of RNA or small nucleic acid fragments,
such as nucleotides, or other contaminants. It is not recommend to use low quality or degraded DNA.

DNA with RNA contamination, results in underestimation of the amount of DNA used. RNase step is
recommended, however, not required to be included with the DNA isolation method.

If there is not enough starting material or enough good quality material available, alternative workflows
exist and can be discussed separately. However, FMSC does not guarantee results for samples with low
DNA quality.
HiSeq2500 sequencing run and result delivery

Sample quality is controlled carefully during the library preparation and only good quality libraries will be
sequenced.

The typical yields are 120-180 x 106 paired-end or single-end reads per lane on HiSeq 2500, depending on
the library type and quality. 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 samples.

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.
HiSeq Sample Submission Form 2015
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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
HiSeq Sample Submission Form 2015
_______________________
Signature
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