RNA-Seq of healthy Sigmodon hispidus large intestine for de novo tran... - SRA

SRX19056416: RNA-Seq of healthy Sigmodon hispidus large intestine for de novo transcriptome assembly, replicate 2
1 ILLUMINA (Illumina NovaSeq 6000) run: 58.8M spots, 17.8G bases, 5.8Gb downloads

Design: In summary, small sections of cotton rat lung (lingular lobe), large intestines (~20 mm colon, flushed with sterile PBS), spleen, kidney, and heart were homogenized using a NextAdvance Bullet Blender with RED RINO tubes containing 3.2 mm stainless steel beads (SSB32) and 2volume of QIAzol Lysis Regent (Qiagen, cat. no. 79306) at max speed for 3 min. RNA was extracted from homogenates using RNeasy Plus Universal Mini kit (Qiagen, cat. No. 73404) via additional QIAzol (total volume 900uL), gDNA eliminator, and chloroform with column DNase digestion as recommend by the manufacturers protocol. RNA quality was measured using an Agilent 2100 Bioanalyzer (Agilent Technologies, CA, USA). Host rRNA was removed using the NEBNext rRNA Depletion Kit v2 (Cat no: NEB E7400X). The cDNA libraries were prepared using 1 g total RNA from each sample using the NEBNext Ultra II RNA Library Prep Kit for Illumina (Cat no: NEB E7805L) following the manufacturers protocol for intact RNA (RIN>7), AMPure XP Beads for cleanup steps (Beckman, cat. No. A63881), and NEBNext Multiplex Oligos for Illumina (Set 1, cat no: E7600S) for pooling samples. Sequencing was performed using Illumina NovaSeq6000 2150 bp sequencing at the Vanderbilt Technologies for Applied Genomics (VANTAGE) core facility.

Submitted by: Vanderbilt University Medical Center

Study: Reference transcriptome and RSV infection in two species of cotton rats: Sigmodon fulviventer and Sigmodon hispidus

PRJNA816878 • SRP417985 • All experiments • All runs

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Background: The cotton rat (Sigmodon) is the gold standard pre-clinical animal model for respiratory viral pathogens, especially for Respiratory Syncytial Virus (RSV). However, without a published genome, transcriptomic analysis in cotton rats is not possible. The aim of this study was to generate a comprehensive de novo transcriptome from multiple organs of two species of cotton rats commonly used in the laboratory (S. fulviventer and S. hispidus) and compare and contrast lung gene expression and immune response changes between the two species upon RSV infection.Results: Our assembly generated nearly 120,000 gene and isoform annotations for each species. Following RSV infection, we identified 279 unique and annotated genes to be up- and down-regulated, including several genes strongly implicated in RSV infection (Mx1, I27L2, IIGP1, LY6E, Viperin, Keratin 6A) as well as novel genes not previously described in RSV research (LG3BP, SYWC, MYO7B, A1CF, APOBEC1, RIC1, KPYR, Claudin-2, and NR1H4)Conclusions: This study presents transcriptome references for future RNA-seq studies in the cotton rat model, as well as provides gene sequences for molecular diagnostics during research. Our differential expression analysis highlights potential targets for RSV pathogenesis, treatment, and prevention.

Sample: 6141-MS-08

SAMN32775668 • SRS16472514 • All experiments • All runs

Organism: Sigmodon hispidus

Library:

Name: 6141-MS-08

Instrument: Illumina NovaSeq 6000

Strategy: RNA-Seq

Source: METATRANSCRIPTOMIC

Selection: Hybrid Selection

Layout: PAIRED

Runs: 1 run, 58.8M spots, 17.8G bases, 5.8Gb

Run	# of Spots	# of Bases	Size	Published
SRR23104983	58,807,554	17.8G	5.8Gb	2023-01-18

ID:: 26227103

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