|
| Status |
Public on Oct 21, 2020 |
| Title |
B6_OMPxvac_Lung_CD4pos_2 |
| Sample type |
SRA |
| |
|
| Source name |
Lung
|
| Organism |
Mus musculus |
| Characteristics |
strain: C57BL/6
time point of infection: without infection
|
| Treatment protocol |
①immunization with OmpX + LTA1 or heat killed Klebsiella pneumoniae (ATCC 43816) twice 3 weeks apart. ②immunization with OmpX + LTA1 twice 3 weeks apart, and 1 more week later infected with 10e4 CFU K1 strain. Those mice were euthanized for lung tissue extraction 4 hours post infetion.
|
| Growth protocol |
All mice were obtained from Jax farm and maintained in specific pathogen-free rooms at Tulane University. Experiment were preformed when mice were at age of six to ten weeks
|
| Extracted molecule |
total RNA |
| Extraction protocol |
mRNA was extracted from lung single cell suspension using the 10X Genomics Chromium™ Single Cell A Chip Kit
Library construction was performed according to 10x Genomics Chromium™ Single Cell 3' Reagent Kit v2 protocol
single cell gene expression RNA-seq
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
NextSeq 550 |
| |
|
| Description |
022219_10x_scRNAseq_LungVaccine_NI&JK
|
| Data processing |
10x Cellranger V.3.1.0 and V.2.1.0 were used to generate Fastq files, perform alignment,filtering,barcode counting,UMI counting and aggregation.
Seurat V.2.3.1 and V.3.0.0 for scRNA QC and further analysis
|
| |
|
| Submission date |
Sep 02, 2020 |
| Last update date |
Oct 21, 2020 |
| Contact name |
Jay Kolls |
| Organization name |
Tulane University
|
| Department |
Medicine
|
| Lab |
Center for Translational Research in Infection and Inflammation
|
| Street address |
1430 Tulane Ave
|
| City |
New Orleans |
| State/province |
LA |
| ZIP/Postal code |
70112 |
| Country |
USA |
| |
|
| Platform ID |
GPL21626 |
| Series (1) |
| GSE157382 |
Subunit vaccine elicited lung TRM cells use fibroblast IL-17R signaling to provide serotype independent immunity against hypervirulent K. pneumoniae |
|
| Relations |
| BioSample |
SAMN15970565 |
| SRA |
SRX9063298 |
