|
| Status |
Public on Dec 29, 2023 |
| Title |
IL4 |
| Sample type |
SRA |
| |
|
| Source name |
Peritoneal cells
|
| Organism |
Mus musculus |
| Characteristics |
cell type: Peritoneal cells
strain: CB6F1/J
age: 6-8 weeks old
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Peritoneal cells were isolated from CB6F1/J (Jax no. 100007) mice after IL4 treatment.
10x Genomics Single Cell Gene Expression libraries were sequenced on a NextSeq 2000 run. The sequencing run was setup as a 28 cycles + 90 cycles non-symmetric run.
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic single cell |
| Library selection |
cDNA |
| Instrument model |
NextSeq 2000 |
| |
|
| Description |
10x Genomics
|
| Data processing |
The analysis was performed with the Cell Ranger 7.1.0 software using the default parameters.
Souporcell (https://github.com/wheaton5/souporcell ) was used to separate the cells from CB6F1/J (Jax no. 100007) into BL/6 and BALB/c cells with singularity exec function.
Seurat (v3.2.3) R package to perform calculation of the number of unique genes detected in each cell (nFeature_RNA), the total number of molecules detected within a cell (nCount_RNA), and produce the UMAP.
pySCENIC (v0.10.) was used to explore the potential transcriptional regulators.
Assembly: mm10
Supplementary files format and content: HDF5 files are provied for further analyisis
|
| |
|
| Submission date |
Nov 16, 2023 |
| Last update date |
Dec 29, 2023 |
| Contact name |
Mingming Zhao |
| E-mail(s) |
mingming.zhao@nih.gov
|
| Organization name |
national institutes of health
|
| Street address |
9000 Rockville Pike
|
| City |
Bethesda |
| ZIP/Postal code |
20892 |
| Country |
USA |
| |
|
| Platform ID |
GPL30172 |
| Series (2) |
| GSE248037 |
Genetic variation in IL-4 activated tissue resident macrophages alters the epigenetic state to determine strain specific synergistic responses to LPS [scRNA-seq] |
| GSE248038 |
Genetic variation in IL-4 activated tissue resident macrophages alters the epigenetic state to determine strain specific synergistic responses to LPS |
|
| Relations |
| BioSample |
SAMN38285661 |
| SRA |
SRX22550212 |
