Effects of a second iron dextran injection administered to piglets during lactation on differential gene expression in liver and duodenum at weaning

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 < 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 < 0.05. Pathway analysis was conducted with Z-score cutoff of P < 0.05. In the duodenum 435 genes were significantly changed with a FC ≥ |1.2| P < 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 adhesi..., RNA Sequencing
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.
Detection of DGE and Bioinformatic Data Handling
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 P < 0.05.
The filtered genes were then subjected to Ingenuity Pathway Analysis (IPA; QIAGEN Inc., Redwo..., , # 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.

本实验选用6头同窝雌性仔猪，旨在评估注射1次或2次右旋糖酐铁（200 mg Fe/mL，每次1 mL）后仔猪组织内的mRNA表达水平。该同窝仔猪均在出生后24小时内接受首次1 mL右旋糖酐铁注射。实验第7天，按体重配对（平均体重=1.72±0.13 kg），每对仔猪中随机选取1头作为对照组（CON），另一头则接受第二次右旋糖酐铁注射（+Fe组）。实验第22天断奶时，对所有仔猪实施麻醉，采集肝脏与十二指肠组织样本并保存，直至mRNA提取环节。
差异基因表达（Differential Gene Expression, DGE）数据以|折叠变化（Fold Change, FC）|≥1.2且P<0.05作为筛选阈值进行分析。通路分析则以P<0.05作为Z值截点。十二指肠中共有435个基因符合|FC|≥1.2且P<0.05的筛选标准，其中紧密连接蛋白1（Claudin 1, CLDN1）与紧密连接蛋白2（Claudin 2）的表达在+Fe组中呈反向变化。CLDN1在细胞间黏附过程中发挥关键作用……（原文此处截断），实验采用RNA测序（RNA Sequencing）技术。
样本送至美国加利福尼亚州欧文市的Zymo Research公司完成总mRNA提取、cDNA文库构建及RNA测序。以250 ng总RNA为起始材料构建总RNA测序文库，采用Bogdanova等于2011年报道的方法去除核糖体RNA（rRNA）。文库制备严格遵循Zymo-Seq RiboFree总RNA文库制备试剂盒（货号R3000）的制造商操作指南（Zymo-Research, 2022）。所有文库在Illumina NovaSeq平台上进行测序，每个样本的测序深度不低于3000万读对（150 bp双端测序）。
差异表达基因的检测采用GeneSpring软件（安捷伦科技，加利福尼亚州圣克拉拉），筛选标准为表达水平的|FC|≥1.2且统计学显著性P<0.05。筛选得到的基因随后进行Ingenuity通路分析（Ingenuity Pathway Analysis, IPA；凯杰公司，雷德伍德……原文截断）。# 泌乳期仔猪二次注射右旋糖酐铁对断奶时肝脏与十二指肠差异基因表达的影响

本数据集包含实验产生的RNA测序原始数据的.BAM格式文件。
## 数据与文件结构说明
本数据集包含按本论文所述流程生成的RNA测序相关文件。
文件名前缀规则如下：
DC：十二指肠对照组样本
DT：十二指肠处理组样本
LC：肝脏对照组样本
LT：肝脏处理组样本
每个处理组设置3个生物学重复，即3头仔猪。
双字母前缀后的数字代表该样本对应的仔猪个体编号。