|
| Status |
Public on Dec 25, 2023 |
| Title |
PD-1 KO bone marrow derived dendritic cells, Mtb infected, 2 |
| Sample type |
SRA |
| |
|
| Source name |
myeloid cells
|
| Organism |
Mus musculus |
| Characteristics |
cell line: myeloid cells
cell type: bone marrow derived dendritic cells
genotype: PD-1 knockout
treatment: infect with Mtb-H37Ra
time: 24 hours
|
| Treatment protocol |
Loosely adherent cells were harvested on day 10 and 2×106 cells were re-seeded in a cell-culture plate and stimulated with 1μg/mL LPS for 24 hours.
2.5×106 BMDCs were seeded at 6-well plates and treated with M.tb H37Ra at a multiplicity of infection of 10.
|
| Growth protocol |
Bone marrow cells isolated from wild-type or PD-1 deficient mice were cultured in 2mL BMDCs culture medium (RPMI 1640 medium supplemented with 15% FBS, penicillin/streptomycin, 20ng/mL GM-CSF, and 10ng/mL IL-4) at 37℃ for 9 days.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
RNA was harvested using RNAiso plus reagent (Takara). 1.3 ug of total RNA was used for the construction of sequencing libraries.
RNA libraries for RNA-seq were prepared using SMARTER mRNA-Seq Library Prep Kit following manufacturer's protocols.
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
DNBSEQ-G400 |
| |
|
| Description |
PD_1_KO_MTB_2
|
| Data processing |
Raw reads were adaptor trimmed and quality controled with trimiomatic
Clean reads were aligned and processed with Hisat2 and Samtools
Alignment result were counted with StrignTie and FeatureCount
Differential analysis were conducted with DeSeq2
Assembly: GRCm38
Supplementary files format and content: tab-delimited text files include normalized counts of each sample
|
| |
|
| Submission date |
Dec 02, 2022 |
| Last update date |
Dec 25, 2023 |
| Contact name |
Bing Yang |
| E-mail(s) |
[email protected]
|
| Organization name |
Huazhong Agricultural University
|
| Department |
College of Vetirinary Medicine
|
| Lab |
Gang Cao's Lab
|
| Street address |
No.1 Shizishan Street, Hongshan District
|
| City |
Wuhan |
| State/province |
Hubei |
| ZIP/Postal code |
430000 |
| Country |
China |
| |
|
| Platform ID |
GPL28457 |
| Series (1) |
| GSE219261 |
Effect of PD-1 knockout on Mtb infection |
|
| Relations |
| BioSample |
SAMN32007053 |
| SRA |
SRX18472560 |
