FREQUENTLY ASKED QUESTIONS

Please email us at info@biospyder.com.

We typically complete a service project in 4-6 weeks after receipt of samples.

Yes, we work with countries from across the globe. Please feel free to contact us no matter what country you’re located in.

Sample preparation and submission forms can be found on the customer page. Please send an email to info@biospyder.com if you need access.

Service project files can be downloaded using these instructions.

A wide range of RNA inputs can be used. For ideal results, target 100ng/uL.

TempO-Seq can be run on cell lysates, isolated RNA, whole blood, blood spotted on filter paper, and FFPE tissue slides, and others. Please contact us to learn more about what samples we can accept.

We generally use charged slides as samples stick better and there is less concern about sample loss. Uncharged can be used with a cover slip.

From the customer page, go to Manifests where you can see all available panels.

S1500+ panels are surrogate transcriptome panels designed to target every known pathway. Our whole transcriptome panels target all protein coding genes.

TempO-Seq data is aligned and delivered without normalization. A variety of methods can be used to normalize TempO-Seq data: Comparison of Normalization Methods for Analysis of TempO-Seq Targeted RNA Sequencing Data.

A count table is required to use any of the quality control and analysis tools, while a sample sheet is not required. However, selecting a sample sheet in tandem with a count table will format the sample names in the same order they appear on the micro-titer plate. Additionally, the ‘Description’ column on the Sample sheet can be used to designate replicates for use in PCA (see User Guide section ‘PCA: Grouping Replicates for PCA’)

Fill out the ‘Description’ column in the Sample Sheet to designate sample replicates. Label each replicate within a group with the same alphanumeric characters (e.g. Liver, Kidney, Group1) and upload the Sample Sheet (see TempO-SeqR User Guide section ‘PCA: Grouping Replicates for PCA).

Alignment times vary based on the number and size of the FASTQ files. Typically, alignments take 1 minute per 5 million reads. However, when under heavy user load the BioSpyder High Performance Computing Cluster may take longer to return results. View the ‘Alignment History’ section on the landing page to see the status of your alignment.

Alignments can fail at two separate points, during FASTQ validation and while mapping sequences to the reference genome. If the alignment email contains the message, “FASTQ validation failed. Alignment process could not complete for user.” there is an issue with the format of one or more FASTQ files. Receiving the message, “Aligning process did not complete.” indicates the alignment failed while mapping sequences to the reference genome. If your alignment fails, please reach out to support@biospyder.com.

File upload speeds are dependent on the size of the file(s) and speed of the internet connection. If files will not upload after a few hours please reach out to support@biospyder.com.

TempO-Seq Portal will treat paired samples as independent.

The raw counts were quantified from the alignments using QuasR (v1.26.0) R Package (Gaidatzis et al., 2015) with the default parameters. You can reference the publication for more details: Gaidatzis D, Lerch A, Hahne F, Stadler MB. QuasR: Quantification and annotation of short reads in R. Bioinformatics 31(7):1130-1132 (2015).