This is a test version of Biostars. For the public version, visit https://www.biostars.org.
SRA data accession

Hi!

I am trying to retrieve the scRNA-seq data from a published paper; they say that they performed scRNA-seq on thousands of cells, but looking at the SRA in NCBI, following the bioproject code of the paper, I was able only to find 8 SRA experiments, regarding the raw sequencing. Since I am looking for the expression data, or at least at the raw data for each single cell, do you know where I should look? The link at the bioproject is https://www.ncbi.nlm.nih.gov/bioproject/?term=PRJNA428979

Thank you!

rna-seq
• 2,228 views • link
updated by ATpoint ATpoint • written by JulianC • JulianC

I tried looking at the metadata associated with this submission but it does not seem complete.

An aliquot of 1ug cDNA taken from 10x Genomics output was taken into library prep following the 1D2 Sequencing of Genomic DNA (SQK-LSK308) protocol provided by Oxford Nanopore. Resulting 1D2 adaptor ligated cDNA was then loaded onto a MinIon FLO-MIN107 flowcell and sequencing performed over 48 hours to obtain raw fast5 files. Basecalling was then performed on subsequent output using Albacore version 2.1.3

So it looks like 10x library was sequenced on ONT. So it is not clear how they handled cell barcode data. You may need to check their publication (is there one) to see if you can glean more information.

• 0 views • link
written by GenoMax GenoMax

2 answers

Have a try at SRA Run Selector you will get the raw data (Run)

• 0 views • link
written by Frédéric Bigey Frédéric Bigey

Actually I did, but also in that page 8 results are shown

• 0 views • link
written by JulianC • JulianC

Not every cell gets its own accession number. It is one accession number per scRNA-seq run which then comprises all the hundreds or thousands of cells that were assayed. The accession number stores the raw sequencing data. Most platforms use barcodes to separate the cells (or rather the reads that originate from one cell). An alternative to downloading data from NCBI is to download as fastq directly from the ENA, see

Fast download of FASTQ files from the European Nucleotide Archive (ENA)

• 0 views • link
written by ATpoint ATpoint

Log in to answer this question.

More posts like this