Transcriptome analysis to compare alternative splicing between control and Ahed-deficient hematopoietic stem and progenitor cells (HSPCs) [RNA-Seq]

We discovered a novel functional gene "Ahed" by screening mutant embryonic stem cells (ESCs). We confirmed that Ahed deletion was disruptive to multiple hematopoietic lineages, and Ahed-deficient HSPCs were unable to reconstitute hematopoiesis in vivo. A search through the biophysical interactions of ORFeome-based complexes 3.0 (BioPlex 3.0) network database indicated a close correlation of Ahed protein in the RNA splicing process. Therefore, we conducted RNA-Seq analysis on triplicate differentiated populations comparing control and Ahed cKO FL LSK cells to verify the reproducibility of our findings. Skewed splicing patterns were observed in diverse transcripts for numerous genes, including PU.1, Ythdf2, Sel1l, and Zfp60, which are known to play important roles in hematopoiesis. Overall design: We performed RNA-Seq analysis on triplicate differentiated populations comparing control or Ahed cKO Lin- Sca1+ c-Kit+ (LSK) cells in E14.5 fetal liver.