Next Gen Sequencing (NGS) Info

(Last Updated: 2/12/2014 SJW)

Illumina Sequencing at GENWIZ

(Updated 2/12/2014 SJW)
(Prices all include QC

DNA Library Prep: $300/sample ($400 if multiplexing)
RNA Library Prep: $350/sample ($450 if multiplexing)

HiSeq2500 Paired End 100bp: $2900 per lane
HiSeq2500 Single End 100bp: $1900 per lane

Illumina Sequencing in Genome Sciences

Sample Receipt/QC (for genomic DNA): $34 per sample

Sample Receipt/QC (for prepared libraries): $8 per sample

DNA Library Prep: $119 per sample
RNA Prep: $101 per sample

HiSeq Paired End 50bp: $1,836 per lane (Hi-Seq ~200M reads)
HiSeq Paired End 100bp: $2,836 per lane
Turnaround is ~10 days (if submitting previously prepared libraries)

MiSeq Paired End 25bp: $953 per run (MiSeq ~15M reads)
MiSeq Paired End 150bp: $1,295 per run

Technician Support: $68 per hour (if their lab does the pooling of samples for sequencing they charge for the personnel time. It usually takes about 1 hour per batch)

UW High-Throughput Sequencing Unit Pricing

(Note: Fastest sequencing option is Illumina HiSeq 36bp, SE)

Illumina HiSeq2000
Library Construction
RNAseq (polyA non-stranded) - $287
DNA TruSeq - $300
RNAseq (stranded SeqScript v2) - $414
Bisulfite DNA TruSeq - $330

Sequencing (per lane; max multiplex = 96 libraries per lane if "homemade"; 25 libraries per lane if made by HTGU)
36bp, SE - $924
72bp, SE - $1497 (Note: Demand is virtually zero. Time frame between runs is unknown, as they have never run this before.)
100bp, SE - $2070

36bp, PE - $1440
72bp, PE - $2449
100bp, PE - $3458

SOLiD 5500xl
Library Construction
RNA - $597
DNA - $372

Sequencing (per lane, if less than 6 lanes; max multiplex = 96 libraries per lane)
50bp, SE - $2374
50bp x 35bp, PE - $3218

Sequencing (per lane, if using all 6 lanes; max multiplex = 96 libraries per lane)
50bp, SE - $1275
50bp x 35bp, PE - $2119

Fred Hutchinson NGS Pricing (Pricing not available on website)

(Note: Fastest sequencing option is 50bp PE; turnaround time of weeks, not months)

Illumina HiSeq2500 (x2)
Library Construction
RNAseq -
DNA -

Sequencing (per lane)
50bp, PE -
100bp, SE - (Note: Demand is extremely low. Time frame between runs for a full slide is ~6-8 months)

8/10/2013 SJW

UW PacBio Sequencing Services (https://pacbio.gs.washington.edu/)

QC & Library Construction - $165
3-10kb C2 Run - $540

Average turnaround time is two weeks.
6/6/2013 SJW

Standard (Single Sample) RNA-Seq Procedure for UW High-Throughput Sequencing Unit (HTGU)

1. Isolate total RNA.
2. DNase treat total RNA.
3. Submit at least 100ng DNase-treated total RNA (ask Steven/Sam for username/password). If submitted sample is shellfish RNA, request two rounds of PolyA enrichment!

3' Targeted, Multiplexed RNA-Seq Procedures

1. Isolate total RNA.
2. DNase treattotal RNA. Go to step 3a or 3b, depending on sequencing method.
3a. Prepare library for Illumina HiSeq RNA-Seq (protocol courtesy of Eli Meyer)
3b. Prepare library for SOLiD RNA Seq (protocol courtesy of Eli Meyer. Note: may no longer be compatible with HTGU SOLiD machine).
4. Submit sample to HTGU for sequencing(ask Steven/Sam for username/password).

Data Description from HTGU

"None of what we gave you has the index read (i.e. barcode) at all, but there are two sets of files,
1 set is the raw files, without any quality trimming or filtering done, these will be a series of files, going from 001.fastq.gz, 002.fastq.gz…..etc…
The other is just a single file, labeled filtered, which is a file that includes all reads that pass quality filters." - from HTGU 8/7/2012