|
| Status |
Public on Nov 01, 2019 |
| Title |
Resting B cells_Mouse 3 |
| Sample type |
SRA |
| |
|
| Source name |
Spleen
|
| Organism |
Mus musculus |
| Characteristics |
mouse strain: C57BL/6
infection: Plasmodium yoelli (Py)
time: 10 days post infection
tissue: Spleen
cell type: Resting B cells
surface markers: CD138loIgDhi
|
| Treatment protocol |
Mice were infected with 1 million Py parasitzed RBCs i.v
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Spleen were harvested, single cell suspension made, ACK lysed and stained for B220, CD19, CD138 and IgD. Cells were sorted on FACS Aria and FACS Fusion cell sorters. RNA extracted using NucleoSpin RNA kit (Takara Bio USA Inc).
RNA libraries were prepared for sequencing using standard Illumina protocols
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
NextSeq 550 |
| |
|
| Description |
Sample name: 7
|
| Data processing |
The quality of sequence reads was assessed using FastQC (http://www.bioinformatics.babraham.ac.uk/projects/fastqc/) and were aligned using STAR aligner82 to the mouse genome version mm10
Differentially expressed genes were identified using Partek GS software and genes with significant changes were filtered using adjusted p- value of 0.05 as threshold
Ingenuity Pathway Analysis software (Qiagen Bioinformatics) was used to identify the underlying molecular pathways and interaction networks that involved the differentially expressed genes.
Genome_build: mm10
Supplementary_files_format_and_content: Normalized counts
|
| |
|
| Submission date |
Jul 19, 2019 |
| Last update date |
Nov 01, 2019 |
| Contact name |
Rahul Vijay |
| E-mail(s) |
rahul-vijay@uiowa.edu
|
| Phone |
3193357576
|
| Organization name |
University of Iowa
|
| Department |
Microbiology and Immunology
|
| Lab |
Butler Lab
|
| Street address |
51 Newton Road
|
| City |
Iowa City |
| State/province |
Iowa |
| ZIP/Postal code |
52242 |
| Country |
USA |
| |
|
| Platform ID |
GPL21626 |
| Series (1) |
| GSE134548 |
RNA sequencing of splenic B cell populations prevalent in Py-infected mice |
|
| Relations |
| BioSample |
SAMN12322757 |
| SRA |
SRX6475024 |
