A Nile Rat Transcriptomic Landscape Across 22 Organs By Ultra-deep Sequencing and Comparative RNA-seq pipeline (CRSP)

We generated the first ultra-deep Nile grass rat RNA-seq data from 60 biopsy samples representing 22 major organs, providing a unique resource and spatial transcriptomic reference (e.g., tissue gene expression baseline) for using Nile grass rat as a model to study human diseases. We collected 59 biopsy samples from 4 Nile grass rats representing 22 major organs (testis, brain, eye, pancreas, bone, thymus, bone marrow, spleen, heat, muscle, adipose, nerve, trachea, bladder, ovary, uterus, esophagus, stomach, liver, intestine, and kidney). Samples were prepared via the Illumina TruSeq RNA protocol. PolyA+ selection was undertaken via RNA purification beads followed by fragmentation for 6 minutes. We performed first and second strand cDNA synthesis and purified with Agencourt AMPure XP beads. We then performed an end repair step. We next adenylated the 3’ ends, ligated Illumina adapters and purified the libraries with AMPure XP beads. Then, we performed cDNA enrichment via PCR (15 cycles). Finally, we validated our libraries via PicoGreen quantification on a Synergy plate reader. Samples were then barcoded and sequenced as paired-end reads on the Illumina HiSeq 3000 sequencer.