|
| Status |
Public on Dec 21, 2023 |
| Title |
BM neutrophils, KO, Rep1 |
| Sample type |
SRA |
| |
|
| Source name |
Mouse bone marrow neutrophils
|
| Organism |
Mus musculus |
| Characteristics |
cell type: Mouse bone marrow neutrophils
genotype: Alkbh5-/-
treatment: 12h after CLP-induced sepsis
|
| Extracted molecule |
polyA RNA |
| Extraction protocol |
Total RNA was isolated from bone marrow neutrophils with TRIzol reagent (Invitrogen) and subjected to Poly(A)+ mRNA purification via Dynabeads mRNA Purification Kit ( Invitrogen) following the manufacturer’s instructions
RNA libraries were prepared for RNA-seq using standard Illumina protocols
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina NovaSeq 6000 |
| |
|
| Data processing |
The adapters and low quality bases were removed.
The Fastq files were aligned to the reference genome (mm10) using Hisat2 (v2.2.1).
Reads mapped to tRNA and rRNA are removed for the following analysis.
Stringtie (v2.1.4) was used to calculate the TPM of each gene to represent their mRNA expression level.
The differential genes were identified by a negative binomial model using the DEseq2 package.
Assembly: mm10
Supplementary files format and content: txt
|
| |
|
| Submission date |
Feb 06, 2023 |
| Last update date |
Dec 21, 2023 |
| Contact name |
Yang Liu |
| E-mail(s) |
yliu@immunol.org
|
| Organization name |
Peking Union Medical College&Chinese Academy of Medical Sciences
|
| Department |
Immunology
|
| Street address |
Dongdan Santiao 5
|
| City |
Beijing |
| ZIP/Postal code |
100005 |
| Country |
China |
| |
|
| Platform ID |
GPL24247 |
| Series (2) |
| GSE224651 |
Effect of depletion of ALKBH5 on transcriptional landscape in bone marrow neutrophils from septic mice |
| GSE224652 |
ALKBH5 |
|
| Relations |
| BioSample |
SAMN33142120 |
| SRA |
SRX19293771 |
