In my lab, mice infected with tuberculosis develop regional inflammation in the first stages of disease. Therefore, to avoid unrepresented sampling (too much or too little inflamation), we want to use the complete lungs for RNA extraction. The issue with using complete lungs however, is that most of them weigh more than 100 mg and therefore clog the silica-gel filters of the Qiagen RNEasy Plus Mini Kit, resulting in low RNA yields (sometimes lower than 100 ng of RNA). The Kit's protocol suggest using 100 mg of tissue using silica-gel columns? Thanks in advance!
What would work for your case (we did something similar with liver) is to homogenize the entire lung with liquid nitrogen, and then use 30-100mg of that homegnate into the kit. That will accurately represent the entire lung equally, and won't overload your columns. Otherwise you might want to look into different homogenization / extraction methods if you want all the RNA from the lung. The MAXI kit is good for this, the mini has smaller columns.
Thanks so much for your answer Craig, I found it extremely helpful.
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