Project description:The balk RNA-seq in WT and Cav3.1 knock-out (KO) mPFC with or without chronic stress was done to detect gene transcripcts assiciated with chronic stress-induced depressive-like bahaviors in mice.
Project description:The bulk RNA-seq in WT and Cav3.1 knock-out (KO) female mPFC with or without chronic stress was done to detect gene transcripcts assiciated with chronic stress-induced depressive-like bahaviors in mice.
Project description:Purpose: Histone demethylase Kdm1a affected mouse SCLC progression through many down-stream factors or pathways. RNA-seq of mouse SCLC cell lines with or without Kdm1a knock-out was used to find the most enriched pathways in Kdm1a knock-out cells Methods: Total mRNA profiles of control (Crispr-V2) or Kdm1a knock-out mouse SCLC cell lines (Kdm1a-sg1, Kdm1a-sg2) were generated by deep sequencing, using Illumina Hiseq platform and 125 bp/150 bp paired-end reads. Index of the reference genome was built using Bowtie v2.2.3 and paired-end clean reads were aligned to the reference genome using TopHat v2.0.12. qRT–PCR validation was performed using TaqMan and SYBR Green assays Results: Using an optimized data analysis workflow, we mapped about 30 million sequence reads per sample to the mouse genome (build mm9). Commonly differential expression after Kdm1a knock-out with two different single guide RNAs to control mouse SCLC cells were selected with a fold change ≥1.5. Conclusions: Our data showed four Rest related pathways, including negative cell proliferation, negative cell differentiation, positive regulation of programmed cell death enriched, in commonly up-regulated genes after Kdm1a knock-out with twe different single guide RNAs. Meanwhile, the commonly down-regulated genes were mostly enriched in neron related pathways. These result illustrated the Kdm1a depletion inhibited mouse SCLC progression, defected its neuroendocrine phenotype through the up-regulation of Rest.