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Sample GSM3370187 Query DataSets for GSM3370187
Status Public on Jan 08, 2019
Title mouse LSEC RNA-seq chow-2
Sample type SRA
 
Source name liver
Organism Mus musculus
Characteristics strain: C57BL/6
tissue: liver sinusoid endothelial cells
phenotype: chow
Treatment protocol mice were fed on NASH diet (D09100301, Research Diets) for 36 weeks
Extracted molecule total RNA
Extraction protocol please see samples description
RNA libraries were prepared for sequencing using standard Illumina and 10X genomics Chromium single cell protocols
 
Library strategy RNA-Seq
Library source transcriptomic
Library selection cDNA
Instrument model BGISEQ-500
 
Description CD11b+ cells were depleted with CD11b microbead (Miltenyi Biotec, cat. No. 130-092-634) according to the manufactures’ instruction after NPCs cell extraction. Continually, LSECs were purified from CD11b- cells by magnetic separation with CD146 microbead (Miltenyi Biotec, cat. No. 130-092-007)).
DESeq2_LSEC_RNA_seq.csv
Data processing FastQC was used to assess the sequencing quality on fastq files.
STAR was used for alignment to generate bam files.
The reads aligned to each gene feature were counted by HTSeq.
R package DESeq2 was used for differential expression analysis.
Single-cell RNA seq data was processed by Seurat package.
Genome_build: mm10
Supplementary_files_format_and_content: Processed data files contain DESeq2-normalized read counts from bulk RNA-seq, UMI count matrices from single cell RNA-seq.
 
Submission date Aug 31, 2018
Last update date Jan 08, 2019
Contact name Jiandie Lin
E-mail(s) jdlin@umich.edu
Phone 7346153512
Organization name University of Michigan
Department Cell & Developmental Biology, Life Science Institute
Lab Jiandie Lin Lab
Street address 210 Washtenaw Ave
City Ann Arbor
State/province MI
ZIP/Postal code 48103
Country USA
 
Platform ID GPL23479
Series (1)
GSE119340 Mapping the molecular signatures of diet-induced NASH and its regulation by the hepatokine Tsukushi
Relations
BioSample SAMN09941445
SRA SRX4630382

Supplementary data files not provided
SRA Run SelectorHelp
Raw data are available in SRA
Processed data are available on Series record

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