|
| Status |
Public on Jan 08, 2019 |
| Title |
mouse LSEC RNA-seq chow-3 |
| 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) |
[email protected]
|
| 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 |
SAMN09941444 |
| SRA |
SRX4630383 |
