Frequently asked questions

Single-base chemistry reports where a modification sits and how much of it is present at that nucleotide. Enrichment methods such as MeRIP-seq report where a mark is enriched across transcripts without resolving individual positions, and arrays report modification levels across a defined transcript set in parallel. Only the first kind of readout supports a conclusion about a specific site.

Yes, and that is the usual arrangement. A screening step — array or enrichment work — narrows a sample set down to the transcripts or conditions that changed, and single-base chemistry then resolves those targets. The two steps are quoted together or run in sequence, depending on how the study is funded and staged.

Total RNA, cultured cells, tissue and blood, including the biofluids and preserved material described on the individual service pages. For cells, tissue, blood and biofluids, RNA can also be prepared by Arraystar after the sample arrives, which is often the safer option when extraction has not been done before.

Send total RNA. Purification steps are where small and structured RNAs are lost, and the workflows are set up for total RNA. If only isolated small RNA is available, discuss it with technical support first: it can sometimes be used, but library preparation depends on how much was lost during purification.

Often, but the workflow decides how much degradation is tolerable, and for site-level chemistry RNA integrity is the more critical factor. FFPE blocks and sections are best sent to Arraystar so that de-paraffinisation and extraction can be handled here; serum and plasma suit enrichment-based work, where the RNA of interest is already enriched in the fluid.

Every sample is assessed for purity and integrity before the experiment. Total RNA is expected to reach OD 260/280 ≥ 1.8 and RIN ≥ 7 with no visible degradation. Sample QC reports are included in the final project reports. If a sample is marginal, a specialist contacts you to decide whether to proceed, replace it, or drop it from the study.

Biological replicates. Differences between individuals with the same apparent phenotype exist even in inbred lines, and a single individual per group cannot show whether a change comes from the experimental condition. For heterogeneous material such as mammalian tissue, plan for more individuals per group rather than relying on repeat measurements of one sample.

The deliverables are listed on each service page, and they follow the readout of that workflow: raw sequencing data files formatted for GEO or SRA submission, QC reports, processed result tables with quantification, the analysis outputs described for that method, and a structured project report. Array projects return normalized intensity data and comparison tables instead of sequencing files.

There are two levels. Standardized analysis is described in the deliverables for each service; in-depth data mining can be discussed and scoped separately. After delivery, questions about a result can be raised with the project number quoted in the correspondence, and the analysis can be re-examined on that basis.

Send the modification or service of interest, the sample type and species, the approximate number of samples and the experimental design to support@arraystar.com or through the request form. The reply is a quotation with a statement of work, the terms and conditions, and a project information sheet; once signed, its number becomes the project number.