RNA-Seq Standard package
- Sample submission: 10ng — 1ug purified RNA (see below).
‘Bioanalyzer QC’ is highly recommended; contact us for information about RNA QC options. - Library preparation: NEBNext Ultra II [Directional] RNA
PolyA* enrichment (included) or ribosomal RNA depletion (extra cost; we can deplete animal and/or bacterial rRNA). - Directional (stranded, default) or non-directional (non-stranded, recommended for input < 20ng total RNA).
- Sequencing: minimum 10M raw reads. 10M and 20M read packages available.
10M read package is recommended for Bacterial sequencing.
Deeper sequencing is available on request (extra cost). - Standard analysis: Read preprocessing, mapping to reference genome, data QC reports including mapping rate and sample
clustering analyses, differential gene expression analysis (DESeq2).
Alternative analysis modes including pathogen discovery are also available; contact us for information.
RNA Input Requirements
| Library type | Transcriptome | Reccommended | Minimum |
|---|---|---|---|
| RNA-Seq - directional | PolyA+ | >= 500ng total RNA, RIN>8 | 10ng total RNA, RIN>7 |
| rRNA-depleted | 100ng - 1 ug total RNA | 10ng total RNA | |
| RNA-Seq - standard | PolyA+ | use directional RNA-Seq or 50-100ng total RNA, RIN>8 | 1ng total RNA, RIN>8 |
| rRNA-depeleted | 100ng - 1 ug total RNA | 10ng total RNA | |
| small-RNA sequencing | small RNAs | >=500ng total RNA or 10ng cell-free RNA (e.g. serum) | 100ng total RNA or 10pg cell-free RNA (e.g. serum) |
Data Analysis
TREx uses computer resources hosted and maintained by the BRC Bioinformatics Facility. Please go to their site for more information, including access to computational resources (hardware and software) and NGS workshops. The User Guide is a wealth of information.More details on the analysis pipeline and software used by TREx are available by request.
EXAMPLE REPORTS
Data Distribution
Data analysis reports (html and xlsx formats) including data QC, raw count tables, and differential expression analysis results will be distributed when a project is complete via Box, Google Drive, and/or email.
Large data files are available on request and will be distributed via Globus or on the BRC Bioinformatics network (user account required).
Raw reads (fastq files) will be archived for at least 5 years by the TREx Facility.
Mapped reads (bam files) will be retained only as required for standard analysis and will be purged on a quarterly basis.
The first distribution of large data files is included in the standard package rates. Repeat requests for distribution of large data files may incur additional fees.
Service pricing
| Description | Internal price (Cornell and Cornell affiliates) | External Price |
|---|---|---|
| RNAseq package (20M reads) Samples 1-24 (ea.) | $280 | Academic/Non-Profit: $350 / Industry: $460 |
| RNAseq package (20M reads) Samples 25+ | $230 | Academic/Non-Profit: $290 / Industry: $380 |
| RNAseq package (10M reads) Samples 1-24 (ea.) | $245 | Academic/Non-Profit: $310 / Industry: $405 |
| RNAseq package (10M reads) Samples 25+ | $195 | Academic/Non-Profit: $250 / Industry: $325 |
| low-input RNAseq package (20M reads), samples 1-24 | $350 | Academic/Non-Profit: $440 / Industry: $575 |
| low-input RNAseq package (20M reads), samples 25+ | $305 | Academic/Non-Profit: $385 / Industry: $500 |
| add rRNA Subtraction (per sample) | $65 | Academic/Non-Profit: $80 / Industry: $105 |
| add 10M additional reads | $90 | Academic/Non-Profit: $115 / Industry: $150 |
| add 20M additional reads | $125 | Academic/Non-Profit: $155 / Industry: $205 |
| Description | Internal price (Cornell and Cornell affiliates) | External Price |
|---|---|---|
| RNA sample cleanup (per sample) | $45 | Academic/Non-Profit: $55 / Industry: $75 |
| Fragment Analyzer (RNA analysis) - per sample | $18 | Academic/Non-Profit: $23 / Industry: $30 |
| FEMTO Pulse (RNA analysis) - per sample | $24 | Academic/Non-Profit: $30 / Industry: $39 |
| TSO cDNA amplification (per sample) | $100 | Academic/Non-Profit: $125 / Industry: $165 |
| Custom lab work (per hour) | $65 | Academic/Non-Profit: $105 / Industry: $105 |
| Consultation and custom data analysis (per hour) | $20 | Academic/Non-Profit: $25 / Industry: $35 |
| Custom projects are available on a limited basis and require pre-approval | ||