GSE153687 Genome-wide identification and differential expression of long non-coding RNAs in hypoxic zebrafish brain

Contributors : Bodhisattwa Banerjee ; Debaprasad KonerSeries Type : Expression profiling by high throughput sequencingOrganism : Danio rerioLong non-coding RNAs (lncRNAs) are now recognized as the master regulators of numerous biological processes. Hypoxia causes oxidative stress and severe and detrimental effects on brain function and acts as a critical initiating factor in the pathogenesis of Alzheimer ’s disease (AD). However, no data are available on the roles of lncRNAs and their target genes under hypoxia in the sub-regions of the fish brain. A group of zebrafish was exposed to hypoxic conditions (1.15±0.6 mg/l of dissolved oxygen), and RNA-seq performed against three regions of both normox ic (7.6±0.4 mg/l) and hypoxic adult zebrafish brain (i.e., forebrain, midbrain, and hindbrain). The raw reads were aligned to the latest zebrafish genome assembly (GRCz11). Various stringent filtration steps were utilized, identifying a total of 18,791, 17,761, and 17,831 multi-exonic lncRNA transc ripts in the forebrain (Fb), midbrain (Mb), and hindbrain (Hb) regions, respectively. BLAST search against the ZFLNC database identified 8114, 7775, and 7816 novel lncRNA transcripts in the Fb, Mb, and Hb regions, respectively. These novel lncRNAs were first classified according to their localizatio n, with the majority (61%) identified as intronic. The novel lncRNAs were relatively lowly expressed. The differential expression pattern was determined in the three brain regions among n...
Source: GEO: Gene Expression Omnibus - Category: Genetics & Stem Cells Tags: Expression profiling by high throughput sequencing Danio rerio Source Type: research