title: Colon tissue lysates from DSS-induced acute colitis in Twist2Cre;Lkb1fl/+ or Lkb1fl/+ mice
design: Colon tissue lysates from DSS-induced acute colitis in Twist2Cre;Lkb1fl/+ or Lkb1fl/+ mice
library_construction_protocol: Distal colon 5-10mm tissue pieces were dissected from each mouse and placed in RNA later.  Mice were treated with 3% DSS in the drinking water for 7 days followed by 3 days recovery.    RNA was extracted using the commercial kit for DNA, RNA and protein purification from Macherey-Nagel.  3′ RNA sequencing was performed by the Biomedicum Functional Genomics Unit at the Helsinki Institute of Life Science and Biocenter, Finland, at the University of Helsinki. 3′ UTR RNAseq 'Bulkseq' is based upon the Dropseq method for single-cell sequencing (Macosko et al., 2015). The method involves priming mRNA with an oligo-dT primer that also contains a 12 bp barcode and an 8 bp unique molecular identifier (UMI) sequence, which can be used to remove PCR duplicates during data analysis. Single-stranded cDNA is then converted to double-stranded cDNA using the template-switch effect, and double-stranded cDNA product is then amplified with PCR and another set of primers (SMART PCR primer). Samples were pooled and PCR sequencing pools were made with Nextera i7 primers and the Dropseq P5 primers.