DOI: 10.5683/sp3/d8yf9v
title: RNAseq reads for Spongilla lacustris and Aphrocallistes vastus osculum experiments

description: &lt;p&gt;Raw FASTQ files for RNAseq reads produced for the differential gene expression analysis in Chapter 3 of the MSc dissertation "Gene expression and sensory structures in sponges: Explorations of sensory-neural origins in a non-bilaterian context" (Mah, 2017). The Aphrocallistes vastus reads were additionally used for genome assembly and annotation in Francis et al. (2023). No proprietary software is required to access the files. The files are compressed by gzip.&lt;/p&gt;

&lt;p&gt;&lt;b&gt;Experimental Design&lt;/b&gt;:&lt;/p&gt;
&lt;p&gt;Two differential gene expression experiments were performed: For Spongilla lacustris, gene expression in pre-oscular sponges (no osculum) were compared to gene expression in juvenile sponges (with osculum). For the glass sponge Aphrocallistes vastus, we compared gene expression in oscular lip tissue compared to body tissue. For all treatments, three replicates were sequenced. &lt;/p&gt;

&lt;p&gt;&lt;b&gt;Methods&lt;/i&gt;:&lt;/b&gt; 
&lt;p&gt;Tissue Collection: Spongilla lacustris gemmules were collected from Lake Rousseau, British Columbia, Canada and grown in M-medium until they reached the pre-oscular stage or juvenile stage. Corresponding pre-oscular and juvenile tissue for three separate individuals of S. lacustris was obtained and sequenced. Specimens of Aphrocallistes vastus were collected at Fraser Ridge, Vancouver Island, Canada using ROPOS, a remotely operated vehicle. The thinner, flexible oscular tissue was manually dissected from the sponge, flash frozen in liquid nitrogen and stored at -80˚C for transport to the University of Alberta. Oscular tissue was obtained from three separate individuals. The same procedure was followed for body tissue. While body tissue was also collected for three separate individuals only one sample corresponded to an oscular tissue sample from the same individual.&lt;/p&gt;

&lt;p&gt;RNA extraction and sequencing: Total RNA was extracted using Single Cell RNA Purification Kit (Norgen Biotek Corp., Thorold, ON, Canada) and quality checked with a Nanodrop ND-1000 (Nanodrop Technologies, Inc., Wilmington, DE, USA) and Agilent 2100 Bioanalyzer (Agilent Technologies, Santa Clara, CA, USA) using the Eukaryote Total RNA Nano assay. cDNA libraries were made from 1 µg of RNA (20 ng/ul) with the TruSeq RNA Library Prep Kit v2 (Illumina, Inc., San Diego, CA, USA) by Delta Genomics (Edmonton, AB, Canada). All six S. lacustris samples (3 replicates each of pre-oscular and juvenile sponges) and six A. vastus samples (3 replicates of body and oscular tissue) were sequenced on an Illumina NextSeq 500 using the NextSeq Series High-Output Kit (Illumina, Inc., San Diego, CA, USA) to obtain 2x150 bp reads at an average depth of 124x. &lt;/p&gt;

&lt;p&gt;&lt;b&gt;Naming convention of files is as follows: &lt;/b&gt;
&lt;p&gt;Spongilla lacustris pre-oscular sponge samples: GGAPON, BagA-PON-2b, Bag6-PON-1 &lt;/p&gt;
&lt;p&gt;Spongilla lacustris juvenile sponge samples: GG17mg, Bag6-Tube2, Bag-AW-2&lt;/p&gt;
&lt;p&gt;Aphrocallistes vastus osculum samples: AV-20-10, AV3-0-6, AV-4-0-6 &lt;/p&gt;
&lt;p&gt;Aphrocallistes vastus body tissue samples: Av2-3_B-2, B2-8, B1-4_2 &lt;/p&gt;
&lt;p&gt; The remaining elements of the file names follow Illumina FASTQ file naming conventions. &lt;/p&gt;
description: <b>Naming convention of files is as follows: </b>
Spongilla lacustris pre-oscular sponge samples: GGAPON, BagA-PON-2b, Bag6-PON-1 
Spongilla lacustris juvenile sponge samples: GG17mg, Bag6-Tube2, Bag-AW-2
Aphrocallistes vastus osculum samples: AV-20-10, AV3-0-6, AV-4-0-6 
Aphrocallistes vastus body tissue samples: Av2-3_B-2, B2-8, B1-4_2 
 The remaining elements of the file names follow Illumina FASTQ file naming conventions.