DOI: 10.5061/dryad.bvq83bkgv
title: Data from: Effects of a second iron dextran injection administered to piglets during lactation on differential gene expression in liver and duodenum at weaning

description: Six female littermate piglets were used in an experiment to evaluate the
 mRNA expression in tissues from piglets given one or two 1 mL injections
 of iron dextran (200 mg Fe/mL). All piglets in the litter were
 administered the first 1 mL injection &lt; 24 hours after birth. On d
 7, piglets were paired by weight (mean BW = 1.72 ± 0.13 kg) and one piglet
 from each pair was randomly selected as control (CON) and the other
 received a second injection (+Fe). At weaning on d 22, each piglet was
 anesthetized, and samples of liver and duodenum were taken from the
 anesthetized piglets and preserved until mRNA extraction. Differential
 Gene Expression data were analyzed with a fold-change cutoff (FC) of |1.2|
 P &lt; 0.05. Pathway analysis was conducted with Z-score cutoff of P
 &lt; 0.05. In the duodenum 435 genes were significantly changed with a
 FC ≥ |1.2| P &lt; 0.05. In the duodenum, Claudin 1 and Claudin 2 were
 inversely affected by +Fe. Claudin 1 (CLDN1) plays a key role in
 cell-to-cell adhesion in the epithelial cell sheets and was upregulated
 (FC = 4.48, P = 0.0423). Claudin 2 (CLDN2) is expressed in cation leaky
 epithelia, especially during disease or inflammation and was downregulated
 (FC = -1.41, P = 0.0097). In the liver, 362 genes were expressed with a FC
 ≥ |1.2| P &lt; 0.05. The gene most affected by a second dose of 200 mg
 Fe was HAMP (Hepcidin Antimicrobial Peptide) with a FC of 40.8. HAMP is a
 liver-produced hormone that is the main circulating regulator of Fe
 absorption and distribution across tissues. It also controls the major
 flows of Fe into plasma by promoting endocytosis and degradation of
 ferroportin (SLC4A1). This leads to the retention of Fe in Fe-exporting
 cells and decreased flow of Fe into plasma. Metabolic pathway changes in
 the duodenum and liver provide evidence for the improved feed conversion
 and growth rates in piglets given two iron injections pre-weaning with
 contemporary pigs in a companion study. In the duodenum, there is a down
 regulation of gene clusters associated with gluconeogenesis (P &lt;
 0.05). Concurrently, there was a decrease in the mRNA expression of genes
 for enzymes required for urea production in the liver (P &lt; 0.05).
 These observations suggest that there may be less need for
 gluconeogenesis, and possibly less urea production from deaminated amino
 acids. The genomic and pathway analyses provided empirical evidence
 linking gene expression with phenotypic observations of piglet health and
 growth improvements.
description: <strong>RNA Sequencing</strong>
 Samples were submitted to Zymo Research (Irvine, CA, USA) for
 total mRNA extraction, cDNA library preparation and RNA sequencing. Total
 RNA-Seq libraries were constructed from 250 ng of total RNA. To remove
 rRNA, a method described by Bogdanova et al., 2011 was followed. Libraries
 were prepared using the Zymo-Seq RiboFree Total RNA Library Prep Kit (Cat
 # R3000) according to the manufacturer’s instructions (Zymo-Research,
 2022). The RNA- Seq libraries were sequenced on an Illumina NovaSeq to a
 sequencing depth of at least 30 million read pairs (150 bp paired-end
 sequencing) per sample. <strong>Detection of DGE
 and Bioinformatic Data Handling</strong>
 Differentially expressed genes were detected using GeneSpring
 software (Agilent, Santa Clara, CA) using selection criteria that accepted
 a DGE threshold of greater than a |1.2|-FC in expression level and
 statistical probability levels of <em>P</em> &lt;
 0.05. The filtered genes were then subjected to
 Ingenuity Pathway Analysis (IPA; QIAGEN Inc., Redwood City, CA;
 https://digitalinsights.qiagen.com/products/) to gain insights into
 canonical pathways, networks, and biological functions. Qiagen IPA uses
 algorithms, tools, and visualizations to combine the directional
 information from gene expression patterns (up- or down-regulation) with
 the expected causal effects of the genes, as reported in the published
 literature. A prediction for effects of a treatment on a particular
 biological pathway function or disease can then be made based upon the
 direction of change in gene expression and calculated Z-scores. Briefly, a
 Z-score is used to compare data that have different means and standard
 deviations. The Z-score is the distance of a point, such as a complete
 pathway, from the mean of the distribution in terms of the standard
 deviation (Corchete et al., 2020; Shao et al., 2020; Wieder, Lai and
 Ebbels, 2022).
description: # Effects of a second iron dextran injection administered to piglets
 during lactation on differential gene expression in liver and duodenum at
 weaning Dataset contains
 .BAM files of the raw data. ## Description of the data and file structure
 This dataset contains the files generated from RNA sequencing as described
 in the manuscript. Files that begin with the following letters are as
 follows: DC - Duodenum Control DT - Duodenum Treatment LC - Liver Control
 LT - Liver Treatment There were three replicates, or pigs, per treatment.
 The number following the two letters represents the individual pig from
 which the sample was taken.