Question: SRA data accession
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gravatar for JulianC
6 months ago by
JulianC10
JulianC10 wrote:

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 • 201 views
ADD COMMENTlink modified 6 months ago by ATpoint34k • written 6 months ago by JulianC10
1

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.

ADD REPLYlink modified 6 months ago • written 6 months ago by genomax83k
0
gravatar for Frédéric Bigey
6 months ago by
Montpellier, France
Frédéric Bigey290 wrote:

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

ADD COMMENTlink written 6 months ago by Frédéric Bigey290

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

ADD REPLYlink written 6 months ago by JulianC10
0
gravatar for ATpoint
6 months ago by
ATpoint34k
Germany
ATpoint34k wrote:

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)

ADD COMMENTlink modified 6 months ago • written 6 months ago by ATpoint34k
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