This is a test version of Biostars. For the public version, visit https://www.biostars.org.
Information on sequin RNA spike in standards

Hi, I am analyzing some publicly available datasets that have used Sequin RNA standards (https://www.sequinstandards.com/rna/) as spike ins. However, I am not able to locate further information about sequins, namely a fasta file for sequin sequences, a gtf file for their annotation as well as their relative abundance (amount) in the mixture. The website link in the original paper (https://www.nature.com/articles/nmeth.3958) does not seem to work.

Can someone provide me with this information or direct me to an appropriate link? Thanks

sequin spike-in rna-seq
• 1,462 views • link
updated by michael.j.apostolides • michael.j.apostolides • written by akainth • akainth

I'd try emailing the authors for a link.

• 0 views • link
written by Ram Ram

1 answer

Very fortunately, someone else has published these sequences on github!

From the paper: "The long and the short of it: unlocking nanopore long-read RNA sequencing data with short-read differential expression analysis tools " https://academic.oup.com/nargab/article/3/2/lqab028/6253498

Github link: https://github.com/XueyiDong/LongReadRNA/tree/master/sequins/annotations

Description of files at that link:

# GTF of sequins

rnasequin_annotation_2.4.gtf

# decoy chromosome (to add to the reference transcriptome, "sequin" reads will align to this and give us our quantities)

rnasequin_decoychr_2.4.fa

# Quantities of each GENE for Mix A and B

rnasequin_genes_2.4.tsv

# Quantities of each ISOFORM for Mix A and B

rnasequin_isoforms_2.4.tsv

# sequin sequences

rnasequin_sequences_2.4.fa

• 0 views • link
written by michael.j.apostolides • michael.j.apostolides

Log in to answer this question.

More posts like this