|
| Status |
Public on Feb 20, 2024 |
| Title |
C1_TgMIF-Mφ_rep1 |
| Sample type |
SRA |
| |
|
| Source name |
RAW264.7 cell line
|
| Organism |
Mus musculus |
| Characteristics |
cell type: mouse leukemia cell of monocyte macrophage
cell line: RAW264.7
treatment: TgMIF-Mφ
|
| Treatment protocol |
RAW264.7 cells were stimulated for 24 h with lipopolysaccharide (LPS, 50 ng/ml, Sigma) and IFN-γ (20 ng/ml), namely LPS/IFNγ-Mφ.
|
| Growth protocol |
cells were cultured in Dulbecco's modified Eagle's medium (DMEM) supplemented with 10% fetal calf serum (FCS).
|
| Extracted molecule |
total RNA |
| Extraction protocol |
RNA was harvested using Trizol reagent. Illumina TruSeq RNA Sample Prep Kit (Cat#FC-122-1001) was used with 1 ug of total RNA for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using standard Illumina protocols
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina NovaSeq 6000 |
| |
|
| Data processing |
Illumina software used for basecalling.
Sequenced reads with low-quality and adapters were trimmed by Trimmomatic-0.39 softeware, then mapped to mm10 whole genome using STAR-2.7.2b with defalt parameters
The unique reads were used to calculate the fragments per kilobase of exon per million fragments mapped (FPKM) with Cufflinks-2.2.1.
Find differential expression genes between stages, HOMER software command getDiffExpression.pl with DESeq2 was employed.
Genome_build: mm10
Supplementary_files_format_and_content: tab-delimited text files include FPKM values for each Sample
|
| |
|
| Submission date |
Mar 01, 2022 |
| Last update date |
Feb 20, 2024 |
| Contact name |
Ying Chen |
| E-mail(s) |
cy.juice@aliyun.com
|
| Phone |
13966667603
|
| Organization name |
Anhui Medical University
|
| Street address |
No. 81 Meishan Road, Hefei
|
| City |
Anhui |
| State/province |
China |
| ZIP/Postal code |
230032 |
| Country |
China |
| |
|
| Platform ID |
GPL24247 |
| Series (1) |
| GSE197639 |
Protozoan-Derived Cytokine-Transgenic Macrophages Reverse Hepatic Fibrosis. |
|
| Relations |
| BioSample |
SAMN26332231 |
| SRA |
SRX14327086 |
