The Microarray and Next-Gen Sequencing Section provides technologies that enable profiling of gene expression, miRNA, GpC Island, and CGH on a whole-genome scale, providing high quality genomics data on Illumina sequencing and microarray platforms. The Genomics and Molecular Biology Shared Resource (GMBSR) is supported by the Norris Cotton Cancer Center at the Dartmouth Geisel School of Medicine.
The Molecular Biology Section provides DNA fragment analysis qPCR, Sanger sequencing and NanoString Technology.
Our facility works closely with investigators to provide outstanding service and support and we strive for rapid turnaround times of 3-6 weeks depending on workload.
More information can be found at our website: geiselmed.dartmouth.edu/gsr
GMBSR offers a variety of RNA-seq library preparation services, depending on the portion of the transcriptome to be interrogated in the experiment. For bacterial samples, ribodepleted libraries must be selected. A list of these services, their merits, input requirements and pricing is provided below.
PolyA Libraries ($330/sample, 100ng Total RNA required): Used for measuring only coding, mRNA transcripts. Not suitable for low quality/degraded samples.
Ribodepleted Libraries ($385/sample, 100ng Total RNA required): Used for measuring mRNA, lncRNA and other RNA forms >140nt. Does not capture miRNAs. Preferred method for FFPE or otherwise degraded samples.
3'-End PolyA ($280/sample, 1-500ng Total RNA required): Used for cost-effective differential gene expression of mRNA transcripts. Lower sequencing depth requirements enables increased multiplexing, decreasing the overall cost per sample.
miRNA/smRNA ($360/sample, 10-100ng Total RNA required): Used to exclusively profile miRNA or other small RNA species ~30-60nt in length.
GMBSR can generate data on all Affymetrix gene expression array platforms. Most commonly we utilize the Clariom S and D arrays for Human, Mouse and Rat samples. For other organisms (ie D. melanogaster), we recommend the GeneChip product.
Users should submit a minimum of 500ng total RNA to provide enough material for QC and labeling. All samples will be subjected to QC by Qubit and Fragment Analyzer prior to to labeling. In the case of low quality samples, users will be notified and will have the option to triage samples or to move forward with labeling.
Data will be provided to users as .CEL files which can be used for downstream analysis.
GMBSR provides services to perform CNV and SNP genotyping analysis on 10,000's - millions of genomic targets through the use of Illumina's Infinium Arrays. In addition, we offer Illumina Infinium Methylation BeadChip arrays that enable the profiling of up to 850,000 methylation sites genome-wide.
These arrays support for FFPE or freshly-prepared DNA and we request a minimum of 500ng of DNA.
Depending on the array requested, 4-24 samples are required per array. Please consult illumina.com or contact GMBSR for details about a particular product.
Pricing is dependent on type of array chosen and number of samples to run. Please inquire for price quote.
Illumina Sequencing is carried out on a NextSeq500 instrument. Pricing includes quantification, normalization and pooling of samples. Please inquire about multiplexing options and compatibility.
All run modes support single or paired-end configurations and custom read lengths.
The following run modes are available:
High Output (400M singe-end reads per run)
75 cycles = $1,900
150 cycles = $3,450
300 cycles = $5,370
Mid Output (130M single-end reads/run)
150 cycles = $1,460
300 cycles = $2,200
RNA extraction can be performed from both fresh and FFPE samples. Unless microRNAs are to to be captured, extraction is performed with the Qiagen RNeasy Mini Plus kit. For isolation of Total RNA (miRNA, lncRNA, mRNA etc.), samples should be provided homogenized in Trizol or frozen as cell/tissue pellets. Samples will be prepared with Zymo directZol columns.
Genomics and Molecular Biology Shared Resources (GMBSR) has not received any reviews.
Genomics and Molecular Biology Shared Resources (GMBSR) has not received any endorsements.