Genome Sciences

Novaseq 6000 is a high throughput sequencer that allows to generate ~750 million reads to 10 billion reads in one run

Miseq is a low throughput sequencer that allows to generate ~1 million reads to 20 million reads in one run

This is for automated capture of single cells from unfixed or fixed cells to perform RNA-seq, ATAC-seq, or both assays. Each well allows capture of 20,000 cells in one well.

iScan is a high throughput scanner for Illumina's mnicroarrays for a wide range of applications including genotyping and DNA methylation quantification

The 4200 TapeStation system is a high-throughput automated electrophoresis platform for nucleic acid sample quality control. It allows analysis of individual samples, up to 96 samples per run to get integrity numbers.

QuantStudio 5 system is a qPCR instrument for detecting differences in gene expression, or genotype alleles. Genome Sciences core has two Quanstudio 5 and are available as self-use instruments. Please schedule the instrument in iLab.

These sample images were provided by Darran May, Aubree Hoover and Tom Sims as part of a presentation on the interpretation of Bioanalyzer 2100 RNA analysis. Similar interpretation also applies to Tapestation profiles too (updated images coming soon!)

Image of Perfect (Intact Eukaryotic) Total RNA

A: 5S subunit; prep-dependent.

B: There maybe a small peak present at approximately 24 seconds that represents 5s, 5.8s and tRNA. This is especially noted with phenol or Trizol extraction, and is eliminated when total RNA is prepped using Qaigen columns, which remove the small RNAs. (Substitute 16S and 23S for prokaryotic samples.)

C: Distinct 18s ribosomal subunit.

D: No small, well-defined peaks between ribosomal peaks.

E: Distinct 28S ribosomal subunit (usually approximately twice 18S).

F: Flat baseline throughout electropherogram.

Samples that result in the above electropherogram image are good to use for message RNA preparation.

Image of Partially Digested Total RNA

A: Intensities of the smaller degraded RNA increases.

B: Baseline between and to the left of the ribosomal peaks becomes jagged.

C: 18s ribosomal subunit.

D: Intensities of the peaks decrease.

E: 28S ribosomal subunit; in general, the 28S peak begins to degrade first.

F: Peak begins to shift toward the left of the electropherogram.

Samples that result in the above electropherogram image are borderline for message RNA preparation and should be under serious consideration of re-extraction.

Image of Severely Degraded Total RNA

A: Overall decrease in fluorescent signal.

B: Ribosomal peaks mostly degraded; generally 28S peak degrades first.

C: Baseline shifts from flat linke to distinct fragmented peaks.

D: Major shift of products toward left of electropherogram as smaller fragments are created by degradation.

Samples that result in the above electropherogram image should not be used to prep message RNA.

Image of Genomic-DNA-Contaminated Total RNA

A: Nano peak.

B: Genomic DNA skewing 8S peak.

C: Additional genomic DNA peak.

The sample may wrongly be considered degraded, and concentration may be inflated. Genomic DNA may interfere with downstream reactions if not removed. Treatment can be done during isolation with QIagen RNase-Free DNase or by post-isolation digestion.

(This sample was provided by Joan Tupper.)

Check back for details.

Check back for details.

The facility receives either tissue/cells, DNA/RNA or customer-generated NGS libraries. Samples are processed based on agreement reached during consultations on the design of the experiment. Well-experienced staff members are available for assisting in project operations. The facility develops new applications to accommodate state-of-the-art NGS technologies.

Additional details will be posted at a later date.

Please check iLab or contact the core at genomesciences@pennstatehealth.psu.edu