title: GSM5026937: Liver_CN16_E2_stdata; Mus musculus; RNA-Seq
library_construction_protocol: mice were euthanized between week 8 and 12, livers were collected, and four lobes were separated. Each lobe was segmented so cryosections would fit on the 6,200 x 6,400 µm areas of the Codelink-activated microscope slides and frozen in -30°C 2-Methylbutane (Merck, cat.no.: M32631-1L). The frozen liver samples were embedded in cryomolds (10x10 mm, TissueTek) filled with pre-chilled (4°C) OCT embedding matrix and frozen (CellPath, cat.no.: 00411243). The sequencing libraries were prepared as described in Jemt et al. (DOI: 10.1038/srep37137 ).In short, the 2nd strand synthesis, cDNA purification, in vitro transcription, amplified RNA purification, adapter ligation, post-ligation purification, a second 2nd strand synthesis and purification were done using an automated MBS 8000+ system. To determine the number of PCR cycles needed for optimal indexing conditions, using qPCR as described previously 58. After determination of the optimal cycle number for each sample, the remaining cDNA was indexed and amplified. The indexed libraries were then purified using an automated system as previously described 60. The average length of the indexed cDNA libraries was determined with a 2100 Bioanalyzer using the Bioanalyzer High Sensitivity DNA kit (Agilent, cat.no.:5067-4626), concentrations were measured using a Qubit dsDNA HS Assay Kit (Thermofisher, cat.no:Q32851) and libraries were diluted to 4nM. Paired-end sequencing was performed on the Illumina NextSeq500 platform