BioMicroCenter:RNA HTL

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HT3DGE method.png

For users with large numbers of eukaryotic RNA samples, The BioMicro Center offers a high-throughput RNAseq methodology that minimizes cost. High-Throughput 3' Digital Gene Expression (HT3DGE) uses a combination of molecular tagged indexes, SMARTseq chemistry and Nextera Tagmentation to produce libraries derived from the 3' ends of transcripts. The protocol is based on Soumillon et al.,doi: as part of a new collaboration with the KI High-Throughput Screening Core. In limiting the sequence space used by the samples, fewer reads should be required for a good transcriptome.

Users bringing their samples in plates must schedule a drop-off time with Austin Hendricks ( to ensure their samples are prepared on the same day.

HT3DGE gene example.png

Plate setup
Batch Size 24
Sample Layout Rows from top
Volume 5ul exact
Concentration 10ng-25ng* totalRNA/5ul
Buffer H2O or 10mM Tris 8.0.
no organics!
Plate Axygen 96well (REF PCR-96-FS-C)
Additional services available
can be added if samples are not submitted as above
  • Sample setup (per 48)
  • SPRI cleanup (if not clean in proper buffer)
  • Advanced Analytical (if not quantified) - 10ul minimim submission..
*Lower input amounts may also work.

HT3DGE uses a very early indexing step to tag each sample with a "well ID" and a molecular ID. Once tagged the samples are immediately pooled to minimize costs but failed samples cannot be easily reprepped and are not identifiable until sequencing. As such, the method is best suited for experiments where the NUMBER of samples is not limiting (material can be). The 3' nature of the protocol also limits the utility of this method in splicing applications but it should be more robust to using imperfect RNA (RIN 7+ instead of 9+ for standard RNAseq)

Analysis of HT3DGE is not a standard method supported by most open source platforms. We have built pipelines to work with this data, but working closely with the Bioinformatics team is highly recommended.