|
| Status |
Public on May 02, 2024 |
| Title |
Liver macrophages from ND-fed mice, bio rep 1 |
| Sample type |
SRA |
| |
|
| Source name |
Liver macrophages
|
| Organism |
Mus musculus |
| Characteristics |
cell type: Liver macrophages
genotype: WT
treatment: Nomal diet
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA from sorted cells was extracted with TRIzol LS reagent and Favorgen RNA Kit (Favorgen)
RNA-seq libraries were prepared using the Nextera XT Kit (Illumina).
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina NextSeq 500 |
| |
|
| Data processing |
Adaptor sequences were removed from raw data using Trimmomatic (ver.0.36.0).
Sequencing reads after trimming were aligned to a mouse reference genome sequence (GRCm38/mm10) in the HISAT2 (ver.2.2.1).
Read counts per gene were calculated using featureCounts (ver.2.0.1) based on GENCODE gene annotation version M25.
The transcripts per million (TPM) normalization was done according to the length of each gene and the sum of mapped reads.
Supplementary files format and content: GRCm38/mm10
Supplementary files format and content: fastq
|
| |
|
| Submission date |
Apr 15, 2024 |
| Last update date |
May 02, 2024 |
| Contact name |
Kenichi Asano |
| E-mail(s) |
asanok@toyaku.ac.jp
|
| Organization name |
Tokyo University of Pharmacy and Life Sciences
|
| Department |
Life Sciences
|
| Lab |
Immune Regulation
|
| Street address |
1432-1 Horinouchi
|
| City |
Hachioji |
| State/province |
Tokyo |
| ZIP/Postal code |
1920392 |
| Country |
Japan |
| |
|
| Platform ID |
GPL19057 |
| Series (1) |
| GSE263973 |
EGR2 is upregulated in monocyte-derived macrophages in MASH liver |
|
| Relations |
| BioSample |
SAMN40973265 |
| SRA |
SRX24266618 |
