title: GSM4291751: 190628_CIRM_Mouse__liver_Hep_4F_Day2_2_T6__rna-seq_4000_pe_150_Paloma_S6_L002; Mus musculus; RNA-Seq
library_construction_protocol: RNA-Seq: Isolated livers were homogenized with a polytrone in Trizol immediately after collecting tissues. The extracted RNA was purified with RNeasy Mini Kit (QIAGEN) from the homogenates with DNaseI tretment (RNase-Free DNase Set, QIAGEN) to get rid of genomic DNA. ATAC-Seq: Frozen liver samples were processed for ATAC-seq using the Omni-ATAC seq protocol [PMID: 28846090]. Briefly, around 20 mg of frozen tissue was used to isolate nuclei via Dounce homogenization followed by density gradient centrifugation. After isolation of nuclei, transposition mixture was added for transposition reaction. SIngle-cell RNA-Seq: Liver cells were isolated after collagenase perfusion as described before [PMID: 29553556] to get single cell suspension. Briefly, hepatocytes and other cells were isolated separately with different gravity of centrifuge and both fractions were mixed at the same number of cells. Then, the mixture was subjected to scRNA-Seq using Next GEM Single Cell 3' kit v3.1 (10x Genomics). RNA-Seq: RNA quality was assessed and all samples had a minimum RNA integrity number (RIN) of 8.6. RNA library preps were prepared using the Illumina TruSeq Stranded Total RNA Sample Prep kit with Ribo-zero Gold (cat. no. RS-122-2301). ATAC-Seq: All ATAC-seq analysis was performed on two biological replicates. Frozen liver samples were processed for ATAC-seq using the omni-ATAC seq protocol (Corces et al, 2017, Nature Methods). Libraries were constructed using published Nextera PCR primers (Buenrostro et al 2013, Nature methods) and checked for quantity on a TapeStation 2200 (Agilent). Single-Cell RNA-Seq: Liver cells were isolated after collagenase perfusion as described before. Briefly, hepatocytes and other cells were isolated separately with different gravity of centrifuge and both fractions were mixed at the same number of cells. Then, these fractions were subjected to scRNA-Seq using Next GEM Single Cell 3' kit v3.1. ATAC-Seq: Libraries were constructed using published Nextera PCR primers [PMID: 24097267] followed by checking the quality on a TapeStation2200 (Agilent). Single-Cell RNA-Seq: Libraries were prepared using Next GEM Single Cell 3' kit v3.1 (10x Genomics). stranded paired-end mRNA-seq; paired-end ATAC-Seq; 10X Genomics Chromium v3 3' Single-Cell RNA-Seq
attributes.tag: GEO Accession
attributes.value: GSM4291751