MASH_Cxcr3-NK Cells RNA-seq Raw Data
Description
In this study we want to compare the gene expression profile of CD49b+CXCR3- NK cells from the liver of ND and CDHFD mice . This comparison will reveal transcriptional signatures of hepatic CD49b+CXCR3- NK cells in CD-HFD responsible for causing liver pathology in MASH.
Files
Steps to reproduce
strain: C57BL/6 age: 8 months diet: CDHFD or ND tissue: liver cell type: hepatic Cxcr3- NK cells Extracted molecule: total RNA Extraction protoco: Samples for RNA-seq were directly sorted in semi-skirted 96-well PCR plate including lysis buffer (2xTCL buffer (Qiagen, #1070498) + RNase-free water + beta-mercaptoethanol (1% total volume)). Library preparation for bulk 3’-sequencing of poly(A)-RNA was done as described previously in Drop-Seq pipeline. Briefly, barcoded cDNA of each sample was generated with a Maxima RT polymerase (Thermo Fisher) using oligo-dT primer containing barcodes, unique molecular identifiers (UMIs) and an adapter. 5’ ends of the cDNAs were extended by a template switch oligo (TSO) and after pooling of all samples full-length cDNA was amplified with primers binding to the TSO-site and the adapter. cDNA was tagmented with the Nextera XT kit (Illumina) and 3’-end-fragments finally amplified using primers with Illumina P5 and P7 overhangs. The P5 and P7 sites were exchanged to allow sequencing of the cDNA in read1 and barcodes and UMIs in read2 to achieve a better cluster recognition. The library was sequenced on a NextSeq 500 (Illumina) with 75 cycles for the cDNA in read1 and 16 cycles for the barcodes and UMIs in read2. Library strategy: RNA-Seq Library source: transcriptomic Library selection: cDNA Instrument model: Illumina NextSeq 500
Institutions
- Southeast UniversityJiangsu, Nanjing