Comparison of oxygen induced retinopathy transcriptomes between Sprague Dawley rats from two vendors

We performed RNA sequencing on whole retinal lysates from Sprague Dawley rat pups from Charles River Laboratories and Envigo that underwent the Penn 50/10 oxygen-induced retinopathy (OIR) model or were room air (RA) controls. RA control and 50/10 OIR retinas underwent next-generation RNA sequencing, n=4/ group. Pairwise comparisons were performed to generate differentially expressed genes between OIR and control groups from the two vendors during the avascular phase of OIR (postnatal day 15) and the neovascular phase (postnatal day 20). 6 sheets included:
1. P15 RA controls Envigo vs RA controls CRL (Envigos used as denominator, a.k.a CRL/Envigo)
2. P20 RA controls Envigo vs RA controls CRL (Envigos used as denominator, a.k.a CRL/Envigo)
3. P15 RA vs OIR CRL (RA= room air control. DEGs as OIR/RA)
4. P20 RA vs OIR CRL (DEGs as OIR/RA)
5. P15 RA vs OIR Envigo (DEGs as OIR/RA)
6. P20 RA vs OIR Envigo (DEGs as OIR/RA)

本研究对来自查尔斯河实验室（Charles River Laboratories, CRL）与英万科（Envigo）的斯普拉格-道利（Sprague Dawley, SD）大鼠幼崽的全视网膜裂解物进行RNA测序。受试幼崽分为两组：一组接受Penn 50/10氧诱导视网膜病变（Oxygen-induced retinopathy, OIR）造模，另一组作为室内空气（room air, RA）对照组。
RA对照组与50/10 OIR模型组的视网膜样本均进行下一代RNA测序，每组样本量为n=4。
本研究通过两两比较，分别在OIR模型的无血管期（出生后第15天，P15）与新生血管期（出生后第20天，P20），对两家供应商来源的OIR组与对照组样本筛选差异表达基因（differentially expressed genes, DEGs）。该数据集共包含6张工作表：
1. 出生后第15天Envigo来源RA对照组 vs CRL来源RA对照组（以Envigo组为参照，即差异基因比值为CRL/Envigo）
2. 出生后第20天Envigo来源RA对照组 vs CRL来源RA对照组（以Envigo组为参照，即差异基因比值为CRL/Envigo）
3. 出生后第15天CRL来源RA对照组 vs OIR模型组（RA为室内空气对照组，差异表达基因以OIR/RA的比值计算）
4. 出生后第20天CRL来源RA对照组 vs OIR模型组（差异表达基因以OIR/RA的比值计算）
5. 出生后第15天Envigo来源RA对照组 vs OIR模型组（差异表达基因以OIR/RA的比值计算）
6. 出生后第20天Envigo来源RA对照组 vs OIR模型组（差异表达基因以OIR/RA的比值计算）