|
| Status |
Public on Apr 30, 2023 |
| Title |
X5 |
| Sample type |
SRA |
| |
|
| Source name |
macrophage
|
| Organism |
Mus musculus |
| Characteristics |
cell type: Bone marrow derived macrophage
strain: C57BL/6
treatment: co-treated IL4 and PF429424 for 24 hours
|
| Treatment protocol |
BMDM treated with IL4, or IL4 + fatostatin, or IL4 + betulin, or IL4 + 25-HC, or IL4 + PF429424, or IL4 + 1,10-Phen for 24 hours.
|
| Growth protocol |
Bone marrow cells were isolated and cultured with DMEM containing 10% (v/v) FBS and 10 ng/ml mouse M-CSF for 5 days to obtain BMDMs.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
BMDM were harvested for RNA extraction using TRIzol. RNA quality was confirmed by Nanodrop measurement of OD 260/280 and 260/230 ratios and stored at -80℃ under ethanol. 1ug RNA was used for RNA-seq library preparation.
RNA libraries were prepared for sequencing using standard Illumina protocols
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
DNBSEQ-T7 |
| |
|
| Data processing |
The sequencing data was filtered with SOAPnuke（v1.5.2） by Removing reads containing sequencing adapter；
Removing reads whose low-quality base ratio （base quality less than or equal to 5）is more than 20%
removing reads whose unknown base （’N’ base）ratio is more than 5%，afterwards clean reads were obtained and stored in FASTQ format
The clean reads were mapped to reference genome using HISAT2（v2.0.4）.
Genome_build: Bowtie2（v2.2.5）was applied to align the clean reads to the reference coding gene set ，then expression level of gene was calculated by RSEM (v1.2.12).
Supplementary_files_format_and_content: The heatmap was drawn by Pheatmap（v1.0.8）according to the gene expression in different samples.Essentially，differential expression analysis was performed using the DESeq2（v1.4.5） with Q value ≤0.05.
|
| |
|
| Submission date |
Nov 07, 2021 |
| Last update date |
Apr 30, 2023 |
| Contact name |
Yinfang Wu |
| E-mail(s) |
yinfangwu@zju.edu.cn
|
| Organization name |
Zhejiang University
|
| Street address |
Yuhangtang RD 866
|
| City |
Hangzhou |
| ZIP/Postal code |
310058 |
| Country |
China |
| |
|
| Platform ID |
GPL28330 |
| Series (1) |
| GSE188356 |
Cholesterol homeostatic regulator SREBP2 promotes macrophage alternative activation and allergic airway inflammation |
|
| Relations |
| BioSample |
SAMN22961528 |
| SRA |
SRX13035850 |
