|
| Status |
Public on Jan 11, 2024 |
| Title |
TLR2-activated IL-10 KO BMDMs sample 2 |
| Sample type |
SRA |
| |
|
| Source name |
Bone marrow derived macrophage
|
| Organism |
Mus musculus |
| Characteristics |
tissue: Bone marrow derived macrophage
|
| Treatment protocol |
on Day 8 post differentiation, BMDMs were left naïve or activted with 50ng/mL Pam3CSK4 (TLR2 Ligand) for 24h
|
| Growth protocol |
bone marrow cells were cultured for 8 days in DMEM +10% FBS+1% pen/step+ glutamine + NaPyr +0.05ng/mL M-CSF
|
| Extracted molecule |
total RNA |
| Extraction protocol |
cells were lysed in trizol, extracted with chloroform. Aqueous phase was mixed 1:1 with 70% ethanol and put onto Qiagen RNAeasy column following the rest of the manufactorer's protocol
Poly-A
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina NovaSeq 6000 |
| |
|
| Description |
Activated KO-2
|
| Data processing |
Adapter sequences were removed from the raw sequencing reads using the tool Cutadapt (https://journal.embnet.org/index.php/embnetjournal/article/view/200).
STAR v2.5.3 was then used to align the trimmed sequencing reads to the mouse genome (mm10) with default parameters.
After sorting the generated SAM files (as the output of alignment) with Picard Toolkit (Picard Toolkit.” 2019. Broad Institute, GitHub Repository. https://broadinstitute.github.io/picard/; Broad Institute), we counted the number of reads mapped to each gene using HTSeq v0.6.1.
Subsequently, we employed DESeq2 v1.26.0 R package to identify significantly differential genes between naïve and TLR2-activated (24h) WT and IL-10 KO BMDMs.
Assembly: mm10
Supplementary files format and content: Read count table
|
| |
|
| Submission date |
Jan 04, 2024 |
| Last update date |
Jan 11, 2024 |
| Contact name |
Rihao Qu |
| Organization name |
Yale University
|
| Street address |
300 George Street
|
| City |
New Haven |
| State/province |
CT |
| ZIP/Postal code |
06511 |
| Country |
USA |
| |
|
| Platform ID |
GPL24247 |
| Series (2) |
| GSE252547 |
Bulk RNA sequencing analysis of WT and IL-10 knockout bone marrow derived macrophage (BMDMs) |
| GSE252549 |
IL-10 |
|
| Relations |
| BioSample |
SAMN39261906 |
| SRA |
SRX23101025 |
