Small RNA Sequencing Standard Package
- Sample submission: 100ng - 1ug purified RNA (lower input is sufficient for cell-free RNA; see below).
‘Bioanalyzer QC’ is highly recommended; contact us for information about RNA QC options. - Library preparation: NEBNext Small RNA.
- Sequencing: minimum 10M raw reads.
Deeper sequencing is available on request (extra cost). - Standard analysis: Read preprocessing, quantification of annotated microRNAs (miRdeep2 using miRBase annotations), data QC
reports including total microRNA counts and sample clustering analyses, differential microRNA detection analysis (DESeq2).
Optional: reads can be mapped to a reference genome on request.
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 |
|---|---|---|
| Samples 1-24 (ea.) | $280 | Academic/Non-Profit: $355 / Industry: $460 |
| Samples 25+ (ea.) | $230 | Academic/Non-Profit: $290 / Industry: $380 |
| add 10M additional reads | $90 | Academic/Non-Profit: $115 / Industry: $150 |
| 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 |
| Custom lab work (per hour) | $65 | Academic/Non-Profit: $105 / Industry: $105 |
| Consultation and custom data analysis (per hour) | $125 | Academic/Non-Profit: $205 / Industry: $205 |
| Custom projects are available on a limited basis and require pre-approval | ||