Transcriptional Regulation & Expression Facility

Services & Pricing :

To place an order, please click here to lauch the sample submision portal (BRC account required).

Pricing Info:
RNA-Seq
smRNA-Seq
ATAC-Seq

General guidelines and Other info:
RNA Input Requirements
Data Distribution

Sample Submission: 10ng — 1ug purified RNA (see RNA input requirements). '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 20M raw reads. 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.

(BRC account required)

Sample Submission: 100ng - 1ug purified RNA (lower input is sufficient for cell-free RNA; see RNA input requirements).
'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.

(BRC account required)

Sample Submission: At least 25k permeabalized nuclei, frozen in storage media. Please contact us for reccommended sample preparation protocol.
Library Preparation:Illumina TDE1 enzyme.
Sequencing: Minimum 20M (PE 2X150) raw reads. Deeper sequencing is available and may be needed to attain recommended coverage (extra cost).
Standard analysis: Read preprocessing, mapping to reference genome, peak calling and annotation, data QC reports including mapping/duplication rates and "fraction of reads in peaks" (FRIP), differential accessibility analysis (DESeq2). Motif enrichment analysis is available upon request.

(BRC account required)

Library Type	Transcriptome	Recommended	Minimum
RNAseq - directional	polyA+ rRNA-depleted	≥ 500ng total RNA, RIN > 8 100ng - 1µg total RNA	10ng total RNA, RIN > 7 10ng total RNA
RNAseq - non-directional	polyA+ rRNA-depleted	use directional RNAseq or 50-100ng total RNA, RIN > 8 same as directional RNAseq	1ng total RNA, RIN > 8 10ng total RNA
small-RNAseq	small RNAs	≥ 500ng total RNA or 10ng cell-free RNA (e.g. serum)	100ng total RNA or 10pg cell-free RNA (e.g. serum)

Custom services are available on a limited basis for additional cost. Please contact us for more information.

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.