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 companies worldwide. Please visit our distributors page to find your local BioSpyder distributor, or contact us for additional help.

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 from the Customer Page.

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

TempO-Seq can be run on cell lysates, isolated RNA, whole blood, blood spotted on filter paper, FFPE tissue slides and other sample types. 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 slides can be used with a cover slip.

From the Customer Page, go to Manifests where you can see all available panels. Public manifest resources are also available on the TempO-Seq Manifests page.

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. See Comparison of Normalization Methods for Analysis of TempO-Seq Targeted RNA Sequencing Data.

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).

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.

Fill out the Description column in the Sample Sheet to designate sample replicates. Label each replicate within a group with the same alphanumeric characters (for example, Liver, Kidney or Group1) and upload the Sample Sheet.

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 “FASTQ validation failed. Alignment process could not complete for user.” there is an issue with the format of one or more FASTQ files. Receiving “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.

We recommend 2–3 million reads per sample.