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Cornell University

Transcriptional Regulation and Expression Facility (TREx)

The Transcriptional Regulation & Expression (TREx) Facility offers end-to-end genomics profiling services. Our RNA-Seq, small-RNA sequencing, and ATAC-Seq packages include library preparation, sequencing, and standard data analysis. RNA-Seq library options include directional (stranded) or standard libraries, with pre-enrichment options including polyA+ selection and rRNA depletion (HMR and/or bacteria). Standard analyses includes preprocessing/QC, mapping, and differential expression analysis.

We encourage researchers to contact us early about new projects, as we can offer guidance on experimental design and sample quality and input requirements. 

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.


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.

Acknowledging BRC services and staff

If you publish data that has been generated with the help of the services we provide, mentioning the Cornell Institute of Biotechnology in the acknowledgments section is very helpful. Here is why. You can also review our authorship guidelines. Please reference the following Research Resource Identifier (RRID): RRID:SCR_022532