|
| Status |
Public on May 01, 2024 |
| Title |
RNA-seq_KO1 |
| Sample type |
SRA |
| |
|
| Source name |
macrophage
|
| Organism |
Mus musculus |
| Characteristics |
cell type: macrophage
genotype: G3bp1mac-/-
|
| Growth protocol |
DMEM, 10% fetal bocine serum, 1×penicilin/streptomycin. Cells were cultured at 37℃ with 5% CO2.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA was extracted using Trizol reagent
Total RNA was extracted followed by library preparation according to Illumina standard instruction (VAHTS Universal V6 RNA-seq Library Prep Kit for Illumina® ). Agilent 4200 bioanalyzer was employed to evaluate the concentration and size distribution of cDNA library before sequencing with an Illumina novaseq6000. The protocol of high-throughput sequencing was fully according to the manufacturer's instructions (Illumina).
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina NovaSeq 6000 |
| |
|
| Data processing |
The RNA is purified by phenol:chloroform extraction.
The raw reads were filtered by Seqtk before mapping to genome using Hisat2 (version:2.0.4). The fragments of genes were counted using stringtie(v1.3.3b) followed by TMM (trimmed mean of M values) normalization. Significant differential expressed genes (DEGs) were identified as those with a False Discovery Rate (FDR) value above the threshold (Q< 0.05)
Assembly: mm39
Supplementary files format and content: tab-delimited with raw counts and FPKM
|
| |
|
| Submission date |
Apr 16, 2024 |
| Last update date |
May 01, 2024 |
| Contact name |
Ye Zhou |
| E-mail(s) |
yzhou1989@126.com
|
| Organization name |
Naval Medical University
|
| Department |
National Key Laboratory of Immunity & Inflammation
|
| Street address |
Xiangyin Road
|
| City |
Shanghai |
| ZIP/Postal code |
200433 |
| Country |
China |
| |
|
| Platform ID |
GPL24247 |
| Series (1) |
| GSE264134 |
Stress granule assembly impairs macrophage efferocytosis [RNA-seq] |
|
| Relations |
| BioSample |
SAMN40985903 |
| SRA |
SRX24276676 |
