|
| Status |
Public on Jan 22, 2020 |
| Title |
ELNDC_1-1 |
| Sample type |
SRA |
| |
|
| Source name |
Liver dendritic cells
|
| Organism |
Mus musculus |
| Characteristics |
strain: C57BL/6
model: Mice fed with MCD diet for 2 weeks
tissue: Liver
|
| Treatment protocol |
Mice fed methioinine and choline deficient diet for 2 weeks were treated with either empty liposomes or curcumin liposomes.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
RNA is extracted from FACS sorted cells using RNeasy micro kit (Qiagen). Quality and quantity of RNA was estimated either using Bioanalyzer (Agilent Technologies). RNA collected from cells was used to prepare and amplify cDNA for RNA sequencing using SMARTer Ultra Low Input RNA Kit for Sequencing - v3 (Clontech Laboratories).
RNA libraries were prepared for sequencing using Nextera XT DNA library prep kit.
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 4000 |
| |
|
| Description |
ELNDC_1
|
| Data processing |
Reads were aligned to the reference mouse genome GRCm38 with STAR (version 2.4.0d).
Gene read counts were quantified against the GENCODE gene model (version M6).
Analysis and differential expression testing was performed with the DESeq2 (version 1.8.1)
Bioconductor package. R package (version 3.2.1) was used to further analysis.
Genome_build: md5
Supplementary_files_format_and_content: Tab-delimited text files include log transformed values for each sample
|
| |
|
| Submission date |
Feb 07, 2017 |
| Last update date |
Jan 22, 2020 |
| Contact name |
Muralidhara Rao Maradana |
| E-mail(s) |
m.maradana@uq.edu.au
|
| Phone |
+61426410837
|
| Organization name |
The University of Queensland
|
| Lab |
Ranjeny Thomas Lab
|
| Street address |
37 Kent St, Woolloongabba
|
| City |
Brisbane |
| State/province |
Queensland |
| ZIP/Postal code |
4102 |
| Country |
Australia |
| |
|
| Platform ID |
GPL21103 |
| Series (2) |
| GSE94592 |
RNAseq of liver dendritic cells targeted with empty liposomes or curcumin liposomes |
| GSE94594 |
NAFLD model |
|
| Relations |
| BioSample |
SAMN06309607 |
| SRA |
SRX2542135 |
