|
| Status |
Public on Aug 18, 2020 |
| Title |
Clec4f- macrophages derived from mice fed a western diet for 24 weeks, 4 |
| Sample type |
SRA |
| |
|
| Source name |
Liver
|
| Organism |
Mus musculus |
| Characteristics |
strain: C57Bl/6J
diet: western diet
time point: 24 weeks
|
| Extracted molecule |
total RNA |
| Extraction protocol |
All Methods listed in Remmerie et al. Osteopontin expression identifies a subset of recruited macrophages distinct from Kupffer cells in MAFLD.. Immunity. 2020.
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina NextSeq 500 |
| |
|
| Description |
Clec4f- macrophages derived from mice fed a western diet for 24 weeks
|
| Data processing |
FastQC v0.11.9 is used to check the quality of the samples
Sequenced reads were then mapped to mm10 transcriptome using HiSat2 v2.2.0 with default parameters and --max-intronlen 1000000
The mapping files were converted into bam files using samtools v1.10 with parameters -l 9
Reads were counted using FeatureCounts v2.0.0 with parameters -s 0
Genome_build: mm10
Supplementary_files_format_and_content: tab-delimited text files including raw counts (output FeatureCounts, only column 1 and 7) for each sample
|
| |
|
| Submission date |
Aug 11, 2020 |
| Last update date |
Aug 19, 2020 |
| Contact name |
Liesbet Martens |
| E-mail(s) |
liesbet.martens@irc.vib-ugent.be
|
| Organization name |
VIB-University of Ghent
|
| Department |
VIB Inflammation Research Center
|
| Street address |
Technologiepark 927
|
| City |
Zwijnaarde |
| ZIP/Postal code |
9052 |
| Country |
Belgium |
| |
|
| Platform ID |
GPL19057 |
| Series (2) |
| GSE156052 |
Osteopontin expression identifies a subset of recruited macrophages distinct from Kupffer cells in the fatty liver. [Bulk RNA Seq] |
| GSE156059 |
Osteopontin expression identifies a subset of recruited macrophages distinct from Kupffer cells in the fatty liver. |
|
| Relations |
| BioSample |
SAMN15792668 |
| SRA |
SRX8926405 |
