DOI: 10.57760/sciencedb.j00139.00042
title: Gene expression matrix related to the study of chicken RNA editome
title: Gene expression matrix related to the study of chicken RNA editome

description: To characterize the repertoire of A-to-I RNA editing sites (RESs) in chicken and investigate its evolutionary and functional features, we generated RNA-Seq data from the domestic chickens (DCs) and its wild ancestors – the red junglefowl (RJFs). 96 RNA samples were collected from 12 different somatic tissues (i.e., eye, heart, kidney, liver, lung, muscle, spleen, and five distinct brain regions, namely, CC – cerebral cortex, CV – cerebellar vermis, CS – corpus striatum, OB – olfactory bulb, and OL – optic lobe) of 13 adult chickens (including 9 DCs and 4 RJFs) and stored in RNAlater at −80°C until use. In addition, to examine catalytic activity of ADARs during chicken editing, we also included 18 RNA samples from chicken embryonic fibroblast cell line UMNSAH/DF-1 (DF-1) with ADAR knockdown or ADARB2 overexpression. RNA was isolated using Trizol reagent (Invitrogen, Carlsbad, CA) and RNeasy Mini Kits (Qiagen, Germantown, MD), purified using magnetic oligo-dT beads, and checked for quality using a Nanodrop spectrophotometer and agarose gel electrophoresis. 150 bp paired-end libraries were then constructed using NEBNext® UltraTM RNA Library Prep Kit for Illumina® (NEB, Ipswich, MA) and sequenced on the Illumina platform after quantification. For the output RNA-Seq data, we trimmed off adaptors and low-quality reads using fastp (v0.20.1). Filtered reads were aligned to the chicken reference genome (galGal6) using HISAT2 (v2.2.1). Expression of genes was measured through StringTie2 (v2.1.4). Gene annotation file was downloaded from Ensembl (v104).
description: To characterize the repertoire of A-to-I RNA editing sites (RESs) in chicken and investigate its evolutionary and functional features, we generated RNA-Seq data from the domestic chickens (DCs) and its wild ancestors – the red junglefowl (RJFs). 96 RNA samples were collected from 12 different somatic tissues (i.e., eye, heart, kidney, liver, lung, muscle, spleen, and five distinct brain regions, namely, CC – cerebral cortex, CV – cerebellar vermis, CS – corpus striatum, OB – olfactory bulb, and OL – optic lobe) of 13 adult chickens (including 9 DCs and 4 RJFs) and stored in RNAlater at −80°C until use. In addition, to examine catalytic activity of ADARs during chicken editing, we also included 18 RNA samples from chicken embryonic fibroblast cell line UMNSAH/DF-1 (DF-1) with ADAR knockdown or ADARB2 overexpression. RNA was isolated using Trizol reagent (Invitrogen, Carlsbad, CA) and RNeasy Mini Kits (Qiagen, Germantown, MD), purified using magnetic oligo-dT beads, and checked for quality using a Nanodrop spectrophotometer and agarose gel electrophoresis. 150 bp paired-end libraries were then constructed using NEBNext® UltraTM RNA Library Prep Kit for Illumina® (NEB, Ipswich, MA) and sequenced on the Illumina platform after quantification. For the output RNA-Seq data, we trimmed off adaptors and low-quality reads using fastp (v0.20.1). Filtered reads were aligned to the chicken reference genome (galGal6) using HISAT2 (v2.2.1). Expression of genes was measured through StringTie2 (v2.1.4). Gene annotation file was downloaded from Ensembl (v104).