AST 2021 SRA uploads to NCBI

This post details the NCBI Sequence Read Archive upload for the sequence data from the AST 2021 experiment. The github for that project is here. This protocol is based on A. Huffmyer’s SRA upload post and Putnam Lab SRA upload protocol. This post includes information on both the RNAseq and smRNAseq SRA uploads.

Because sample AST-1105 did not sequence well, I am not including it in the data upload. The file itself seems to be corrupt.

Overview for RNAseq uploads

Below is the following information for this submission.

Sequence Read Archive (SRA) submission: SUB15150405

Submitter

Jill Ashey; 120 Flagg Road, Kingston RI 02881

General info

Not associated with current BioProject
Not associated with current BioSample
Release date: immediately

Project info

Project title: Astrangia poculata RNA-seq across seasons
Public description: RNA-seq data from Astrangia poculata 2021 experiment exposing adults to chronic thermal stress across seasons (February - August)
Not associated with umbrella project

Biosample type: invertebrate

Link to submission spreadsheet

Important note so that errors do not occur during upload: After filling out values for attributes provided in the template, your samples are not distinguishable by at least one, or a combination of attributes. Make the combined value of all attributes unique for each sample while taking into account that “sample name”, “sample title” and “description” are not included in this check for “uniqueness”.

SRA metadata

Complete

Files

Upload the fastq.gz files to NCBI with the following code. First, make a new folder that only contains sequence data.

cd /data/putnamlab/jillashey/Astrangia2021/mRNA
mkdir raw_file_rnaseq_sra
cd raw_file_rnaseq_sra

ln -s /data/putnamlab/jillashey/Astrangia2021/mRNA/data/raw/*fastq.gz .
rm *1105* # sample that did not sequence well

Use FTP command line file upload to provide files. Activate FTP on the command line. Command prompt now changes to ftp>. Immediately login using the username and password from the NCBI submission portal.

ftp -i
open ftp-private.ncbi.nlm.nih.gov
USERNAME
PASSWORD 

Go into the folder that NCBI provided from the NCBI submission portal. Make a new directory for the files and go into that folder. Put all the sequences from Andromeda into this new folder (they will still be on Andromeda after transfer is complete).

cd uploads/jillashey_uri.edu_XXXXXXXXXXX
mkdir astrangia_2021_rnaseq
cd astrangia_2021_rnaseq
mput *

This takes a few minutes. Once transfers are complete, click select preload folder in the submission portal. Wait until all files have been uploaded and select the astrangia_2021_rnaseq folder. Click submit!

Bioproject: PRJNA1231118

Overview for smRNAseq uploads