Next+Gen+Sequencing+Info

=__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)

__Library Construction__ RNAseq (polyA non-stranded) - $287 DNA TruSeq - $300 RNAseq (stranded SeqScript v2) - $414 Bisulfite DNA TruSeq - $330
 * __Illumina HiSeq2000__**

__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 treat]total 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

Libraries Made
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