Platform:
Illumina HiSeq Sequencing
Category:
Single End 100 cycle sequencing
Primary Contact: Typical Cost:
Internal

$1300 per lane

External

$1677 per lane

 

Typical Output:

20 Gb

How to request:

Sample Submission: login through https://client-seqcore.brcf.med.umich.edu/ then choose ‘Illumina Sequencing’​

Sample requirements:

30 ul of 10nM Illumina library with and insert size of at least 100 bp

Typical Turnaround:

The run itself takes about 8 days. This is a rare run type for us we would have to fill all 8 lanes of a flow cell before we could run this which could take months.

Platform:
Illumina HiSeq Sequencing
Category:
Single end 50 cycle sequencing
Primary Contact: Typical Cost:
Internal

$986 per lane

External

$1271.94 per lane

 

Typical Output:

10 Gb

How to request:

Sample Submission: login through https://client-seqcore.brcf.med.umich.edu/ then choose ‘Illumina Sequencing’​

Sample requirements:

30 ul of 10nM Illumina library with and insert size of at least 50 bp

Typical Turnaround:

The run itself takes 4.9 days and in general turnaround is 3-4 weeks

Critical information:

It is important that we know if you are working with an unbalanced genome or have modified your library prep in any way.

Platform:
Illumina HiSeq Libraries
Category:
Small RNA Sequencing
Primary Contact: Typical Cost:
Internal

$218 per sample + $19 per sample to multiplex

External

$281.22 per sample + $24.51 per sample to multiplex

 

Typical Output:

Illumina ready library.

How to request:

Sample Submission: login through https://client-seqcore.brcf.med.umich.edu/ then choose ‘Illumina Sequencing’

Sample requirements:

Good quality total RNA 100ng in 10ul

Typical Turnaround:

3 weeks

Critical information:

Only profiling of small RNA can be done using this prep. 

More information:

Please discuss your RNA Seq project with your bioinformaticist or contact the University of Michigan's Bioinformatics Core (bioinformatics@umich.edu) before you begin your project.

For kit information please see NEB's site:

https://www.neb.com/products/e7330-nebnext-small-rna-library-prep-set-fo...

Platform:
Illumina HiSeq Libraries
Category:
Gene Expression Profiling
Primary Contact: Typical Cost:
Internal

$172 per sample + $19 per sample for multiplexing

External

$221.88 per sample + $24.51 per sample to multiplex

 

Typical Output:

The SMARTer stranded kit will yield an Illumina ready to sequence library with an insert size of 180bp 20 ul of ~10nM.

How to request:

Sample Submission: login through https://client-seqcore.brcf.med.umich.edu/ then choose ‘Illumina Sequencing’

Please deliver RNA to NCRC. Courier service from other sites will not guarantee proper temp is maintained!

Sample requirements:

The total fraction of 100pg – 100ng full length, intact total RNA that has been depleted of ribosomal RNA.

This kit has a separate protocol to deal with degraded RNA Samples, such as FFPE RNA which decreases the fragmentation time.

Typical Turnaround:

3 weeks.

Critical information:

Requires ribosomal removal:

 

Ribo Gone requires 10-100ng total RNA abd us the ribosomal removal kit for human mouse and rat available by Clontech:

http://www.clontech.com/US/Products/cDNA_Synthesis_and_Library_Construction/Next_Gen_Sequencing_Kits/Ribosomal_RNA_Removal

 

The SMARTer stranded protocol has been optimized for cDNA synthesis starting from 10pg of total RNA. However if you RNA sample is not limiting, Clontech recommend that you start with more total RNA (up to 10 ng). Purified total RNA should be in nuclease free water.

Platform:
Illumina HiSeq Libraries
Category:
Gene Expression Profiling
Primary Contact: Typical Cost:
Internal

$258 per sample + $19 per sample for multiplexing

External

$332.82 per sample + $24.51 per sample to multiplex

 

Typical Output:

The SMARTer non stranded kit will yield 2-10ng of cDNA between 400 and 100 bp 20-50ul of prepared library

How to request:

Sample Submission: login through https://client-seqcore.brcf.med.umich.edu/ then choose ‘Illumina Sequencing’

Please deliver RNA to NCRC. Courier service from other sites will not guarantee proper temp is maintained!

Sample requirements:

10pg – 10ng total RNA 

Typical Turnaround:

3 weeks

Critical information:

The SMARTer protocol has been optimized for cDNA synthesis starting from 10pg of total RNA. However if you RNA sample is not limiting, Clontech recommends that you start with more total RNA (up to 10 ng). Purified total RNA should be in nuclease free water.

More information:

Due to the two rounds of amplification in this prep the duplicate rate will be higher than normal RNA Seq libraries.

Please discuss your RNA Seq project with your bioinformaticist or contact the University of Michigan's Bioinformatics Core (bioinformatics@umich.edu) before you begin your project.

For kit information please see Clontech's site:

http://www.clontech.com/US/Products/cDNA_Synthesis_and_Library_Construct...

Platform:
Illumina HiSeq Libraries
Category:
Gene Expression Profiling
Primary Contact:

Jeanne Geskes
jgeskes@umich.edu
734-763-4144

Typical Cost:

Customer provides ribosome removal kit.

Internal

$154 for library prep + $19 per sample to multiplex.

External

$198.66 per sample + $24.51 per sample to multiplex

 

Typical Output:

~30 ul of 10nM prepared library with a 120 bp insert, you will also get TapeStation reports of the quality of your input RNA and the resultant library.

How to request:

Submit samples here: http://seqcore.brcf.med.umich.edu/cgi-bin/Solexa/login.cgi

Please deliver RNA to NCRC. Courier service from other sites will not guarantee proper temp is maintained!

Sample requirements:

1ug of good quality, RINs of 8 or higher (add link to FAQ about RNA quality) DNase treated total RNA in 25-50ul OR 1ug of total RNA that has been ribosomal depleted

Typical Turnaround:

2-3 weeks

Critical information:

RNA must be delivered on dry ice to NCRC and cannot be left at our pick sites on campus.

Using ribosomal removal is an option for those samples where poly A purification is not available. The lincRNAs will be retained in this prep.

More information:

Epicentre offers RiboZero kits and has the following selection guide to help you choose the proper kit:

http://www.epibio.com/applications/rna-sequencing/rrna-removal/ribo-zero-and-globin-zero-kit-selection-guide

Ribo-Zero kits remove ribosomal RNA (rRNA) using a hybridization/bead capture procedure that selectively binds rRNA species using biotinylated capture probes. The probe:rRNA hybrid is then captured by magnetic beads and removed using a magnet, leaving the desired rRNA-depleted RNA in solution.

Life Technologies offers RiboMinus:

http://www.lifetechnologies.com/us/en/home/life-science/dna-rna-purifica...

Platform:
Illumina HiSeq Libraries
Category:
Gene Expression Profiling
Primary Contact: Typical Cost:
Internal

$156 per sample + $19/sample to multiplex samples

External

$201.24 per sample + $24.51 per sample to multiplex

 

Typical Output:

~30 ul of 10nM prepared library with a 120 bp insert, you will also get TapeStation reports of the quality of your input RNA and the resultant library.

How to request:

Sample Submission: login through https://client-seqcore.brcf.med.umich.edu/ then choose ‘Illumina Sequencing’

Please deliver RNA to NCRC. Courier service from other sites will not guarantee proper temp is maintained!

Sample requirements:

100ng -4ug of good quality, RINs of 8 or higher, DNase treated total RNA in 25-50ul

Typical Turnaround:

2-3 weeks

Critical information:

RNA must be delivered on dry ice to NCRC and cannot be left at our pick up sites on campus.

More information:

Please discuss your RNA Seq project with your bioinformaticist or contact the University of Michigan's Bioinformatics Core (bioinformatics@umich.edu) before you begin your project.

For kit information please see Illumina's site:

http://www.illumina.com/products/truseq_stranded_mrna_sample_prep_kit.ilmn

Platform:
Illumina HiSeq Libraries
Category:
Gene Expression Profiling
Primary Contact: Typical Cost:
Internal

$110 per sample + $19 per sample to multiplex

External

$141.90 per sample + $24.51 per sample to multiplex

 

Typical Output:

~30 ul of 10nM prepared library with 120bp insert, you will also get TapeStation reports of the quality of your input RNA and the resultant library.

How to request:

Sample Submission: login through https://client-seqcore.brcf.med.umich.edu/ then choose ‘Illumina Sequencing’

Please deliver RNA to NCRC. Courier service from other sites will not guarantee proper temp is maintained!

Sample requirements:

100ng -4ug of good quality, RINs of 8 or higher (add link to FAQ about RNA quality) DNase treated total RNA in 25-50ul

Typical Turnaround:

2-3 weeks

Critical information:

RNA must be delivered on dry ice to NCRC and cannot be left at our drop off sites on campus.

More information:

Please discuss your RNA Seq project with your bioinformaticist or contact the University of Michigan's Bioinformatics Core (bioinformatics@umich.edu) before you begin your project.

For kit information please see Illumina's site:

http://www.illumina.com/products/truseq_rna_sample_prep_kit_v2.ilmn

 

 

Platform:
Ion Proton Sequencer
Category:
Exome Sequencing
Primary Contact:

Suzanne Genik genik@umich.edu 734-764-8067

Typical Cost:

$940.00 per chip (not include tech time), two bar coded sample libraries per chip

Typical Output:

Raw data: 10Gb of data per run

Run time 2-4 hours

Data file formats: BAM, FASTQ, and VCF

Read length up to 200 bp,

Number of reads passing filter is 60-80 Million

Approximate average read depth:

Running one exom sample per chip average coverage about 240X,

Running two exome samples per chip average coverage about 120X,

Running three exome samples per chip average coverage about 80X,

Running two exomes per Ion PI chip, usually see an average of 20X at 95-98%.

98% of target bases are covered at 10X and 94% of targeted bases at are covered at 20X ,

The actual read depth per sample may vary as a result of barcode balance and chip loading.

How to request:

Sample Submission: login through https://client-seqcore.brcf.med.umich.edu/ then choose ‘Fragment Analysis Service’​

Sample requirements:

50 to 200 ng of gDNA at a concentration of 10ng/ul.

Typical Turnaround:

1 to 2 weeks

More information:

The Ion Proton Sequencer uses semiconductor sequencingtechnology as a method for sequencing DNA.The synthesis of sequences are generated through themeasurement of the direct release of H+(Protons).

The semiconductor chips containing microwells with templateDNA strands. Each time a nucleotide is incorporated in thesequence it triggers the release of a hydrogen ion.The release of a hydrogen ion in the reaction changes the pHof the reaction.

A series of electrical pulses from the chip is transmits to acomputer. The pulses are transmitted into a DNA sequence.

The Ion AmpliSeq technology uses a Exome Panel Kit of 12Primer pools in the construction of the Amplicon libraries.The PCR amplification of genomic target regions produce arange of DNA fragments between 200-400bp.The library is amplified using emulsion PCR.

Website source for Ion Proton