|
| Status |
Public on Jan 01, 2020 |
| Title |
TLR4KO-Con |
| Sample type |
SRA |
| |
|
| Source name |
Hepatic stellate cell
|
| Organism |
Mus musculus |
| Characteristics |
strain: C57BL/6
cell: Primary hepatic stellate cell
genotype: TLR4-/-
|
| Treatment protocol |
24-week-old male wild-type, TLR4-/-, and CD44-/- mice were used. All procedures were approvd by the Institutional Animal Care and Use Committee at Cedars-Sinai Medical Center. Hepatic stellate cells were isolated from the mice in a 2-step process: collagenase-pronase perfusion of mouse livers followed by Nycodenz 2-layer discontinuous density gradient centrifugation. We further depleted contaminated liver macrophages by magnetic antibody cell sorting (Miltenyi Biotec) using Cd11b-conjugated microbeads (Miltenyi Biotec).
|
| Growth protocol |
Primary hepatic stellate cells were isolated from male wild-type, TLR4-/-, and CD44-/- mice. After, the isolated primary hepatic stellate cells were incubated in DMEM medium containing 10% FBS, and supplemented with Antibiotic-Antimycotic for 3 days, serum was deprived for 24 hr.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA was extracted using TRIzol (Invitrogen) and purified using RNA isolation kit (Macherey-Nagel). Beijing Genomics Institute (BG) (Beijing, China) performed the RNA sequencing.
RNA libraries were prepared for sequencing using standard BGISEQ-500 protocols
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
BGISEQ-500 |
| |
|
| Data processing |
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to mm10 whole genome using version 2.2.5 with parameters--phred64 --sensitive --dpad 0 --gbar 99999999 --mp 1,1 --np 1 --score-min L,0,-0.1 -p 16 -k 200
Fragments Per Kilobase Million(FPKM) were calculated using RSEM
Genome_build: mm10
Supplementary_files_format_and_content: Excel files include FPKM values for each Sample.
|
| |
|
| Submission date |
Jan 15, 2018 |
| Last update date |
Jan 01, 2020 |
| Contact name |
Ekihiro Seki |
| E-mail(s) |
Ekihiro.Seki@cshs.org
|
| Organization name |
Cedars-Sinai Medical Center
|
| Department |
Medicine
|
| Street address |
8700 Beverly Blvd DAVIS, Suite 2029
|
| City |
Los Angeles |
| State/province |
CA |
| ZIP/Postal code |
90036 |
| Country |
USA |
| |
|
| Platform ID |
GPL23479 |
| Series (1) |
| GSE109200 |
TLR4 or CD44 deficiency effect on hepatic stellate cells |
|
| Relations |
| BioSample |
SAMN08366019 |
| SRA |
SRX3584897 |
