Compartment-specific total RNA profile of Hippocampal and Cortical cells from Mesial Temporal Lobe Epilepsy tissue

Mesial temporal lobe epilepsy (mTLE) is a chronic neurological disease characterized by recurrent seizures. The pathogenic mechanisms underlying TLE involve defects in post-transcriptional regulation of gene expression. So far, transcriptome profiles from epileptic tissue have been performed using whole cells, thereby lacking information on RNA localization and function at a subcellular level. In this project, we set out to understand the compartment-specific total RNA profile of human mTLE tissue samples. For this, we had established a protocol to isolate cytoplasmic and nuclear compartments from human hippocampal tissue. Subcellular RNA was isolated from resected hippocampal (HC) and neo-cortical (Cx) tissue from mTLE no hippocampal sclerosis (non-HS) and mTLE HS International League Against Epilepsy (ILAE) Type 1 or mTLE+HS patients and postmortem control tissue. Later, we used total RNA sequencing (RNA-seq) to profile for the distinct RNA localization in mTLE in comparison to postmortem control tissue and identified disease related pathways in individual cell compartments. Here we report the total RNAseq (coding and non-coding) data. Overall design: We established a protocol to isolate pure nuclear and cytoplasmic fractions from human tissue. After quality controlling for purity of the isolated cell compartments, we performed total RNA-sequencing (RNA-seq) using illumina platform on five HC mTLE non-HS and five HC postmortem controls. Similarly, neo-cortical (Cx) tissue samples from six mTLE non-HS and six mTLE+HS samples and six Cx postmortem controls. From the data obtained, differential gene expression analysis was performed to identify mTLE specific transcript changes among subcellular compartments. Pleaes note that each processed data file was generated from multiple samples as indicated in the file name: Cortex(Cx)_Cytoplasm(cyt)_Control(CTL) & mTLE non-HS(W0) Cortex(Cx)_Cytoplasm(cyt)_Control(CTL) & mTLE+HS(W4) Cortex(Cx)_Cytoplasm(cyt)_PREvsPOST Cortex(Cx)_Hippocampus_Cytoplasm(cyt)_Control(CTL)_vs_mTLE_non-HS & mTLE+HS(W4) Cortex(Cx)_Hippocampus_Cytoplasm(cyt)_Nucleus(Nuc)_Control(CTL)_vs_mTLE non-HS & mTLE+HS(W4) Cortex(Cx)_Nucleus(nuc)_Control(CTL) & mTLE non-HS(W0) Cortex(Cx)_Nucleus(nuc)_Control(CTL) & mTLE+HS(W4) Cortex(Cx)_Nucleus(nuc)_PREvsPOST Hippocampus(Hip)_Cytoplasm(cyt)_Control(CTL) & mTLE non-HS(W0) Hippocampus(Hip)_Nucleus(nuc)_Control(CTL) & mTLE non-HS(W0) Hippocampus(hip)_vs_Cortex(Cx)_cytoplasm(cyt)_circRNA_differentially_expressed(DE) Hippocampus(hip)_vs_Cortex(Cx)_nucleus(nuc)_circRNA_differentially_expressed(DE) mTLE+HS(W4)_vs_mTLE_non-HS(W0)_Cortex(Cx)_cytoplasm(cyt)_circRNA_differentially_expressed(DE) mTLE+HS(W4)_vs_mTLE_non-HS(W0)_Cortex(Cx)_nucleus(nuc)_circRNA_differentially_expressed(DE) nucleus(nuc)_vs_cytoplasm_Cortex(Cx)_circRNA_differentially_expressed(DE) nucleus(nuc)_vs_cytoplasm_hippocampus(hip)_circRNA_differentially_expressed(DE)