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02_smokingMouse_experiment.Rmd

@@ -35,7 +35,7 @@ Nowadays, maternal smoking during pregnancy (MSDP) is one of the major health co
 ## Overview
 This study consisted of a series of bulk RNA-sequencing experiments performed on brain samples from adult mice and pups and on blood samples from adults. Adult mice were either exposed to cigarette smoke (what we call smoking experiment and smoking mice) or controls of the smoking experiment, or they were administered nicotine (nicotine experiment and nicotine mice) or controls of the nicotine experiment, and they were either pregnant or not. Smoking, nicotine and control pups are pups that were born to smoking, nicotine and control pregnant mice, respectively. This experimental design allowed us to contrast the altered features in both conditions and to compare the effects in different mouse ages, sexes, tissues and pregnancy states. 
 
-The original datasets contain gene, transcript, exon and junction expression levels across 208 samples, but in this course we'll only use gene data in nicotine samples to simplify the analyses.
+The original datasets contain gene, transcript, exon, and exon-exon junction expression levels across 208 samples, but in this course we'll only use gene data in nicotine samples to simplify the analyses.
 
 ## Goals
 
@@ -53,7 +53,7 @@ The main goal was to identify and differentiate the effects of prenatal nicotine
 Check [here](https://github.com/LieberInstitute/smokingMouse_Indirects/tree/main/code) for the code of the original and complete analyses done.
 
 ## Study design
-As presented in **Figure 1: A)**, 36 pregnant dams and 35 non-pregnant female adult mice were either administered nicotine by intraperitoneal injection (IP; n=12), exposed to cigarette smoke in smoking chambers (n=24), or controls (n=35; 11 nicotine controls and 24 smoking controls). A total of 137 pups were born to pregnant dams: 19 were born to mice that were administered nicotine, 46 to mice exposed to cigarette smoke and the remaining 72 to control mice (23 to nicotine controls and 49 to smoking controls). Samples from frontal cortices of P0 pups and adults were obtained, as well as blood samples from smoking-exposed and smoking control adults. Then, as shown in **B)** RNA was extracted from all those samples and RNA-seq libraries were prepared and sequenced to obtain expression counts for genes, exons, transcripts and exon-exon junctions.
+As presented in **Figure 1: A)**, 36 pregnant dams and 35 non-pregnant female adult mice were either administered nicotine by intraperitoneal injection (IP; n=12), exposed to cigarette smoke in smoking chambers (n=24), or controls (n=35; 11 nicotine controls and 24 smoking controls). A total of 137 pups were born to pregnant dams: 19 were born to mice that were administered nicotine, 46 to mice exposed to cigarette smoke and the remaining 72 to control mice (23 to nicotine controls and 49 to smoking controls). Samples from frontal cortices of P0 pups and adults were obtained, as well as blood samples from smoking-exposed and smoking control adults. Then, as shown in **B)** RNA was extracted from all those samples and RNA-seq libraries were prepared and sequenced to obtain expression counts for genes, exons, transcripts, and exon-exon junctions.
 
 <figure>
   <img src="http://research.libd.org/smokingMouse/reference/figures/Study_design.png" align="center" width="800px" />