|
| Status |
Public on Apr 06, 2024 |
| Title |
PBS1 |
| Sample type |
SRA |
| |
|
| Source name |
Lung
|
| Organism |
Mus musculus |
| Characteristics |
background strain: BALB/c
tissue: Lung
treatment: PBS
treatment time: 14 days
|
| Treatment protocol |
BALB/c mice were anesthetized and treated with PBS or C. neoformans H99 cell suspension at 5 × 104 cells/mouse by the intranasal route. The activity of the arginase enzyme was inhibited before and after infection by intraperitoneal injection of arginase inhibitor, nor-NOHA (N-hydroxy-nor-L-arginine) daily at 17 mg/kg /day (300 µg/100 µl PBS/mouse). At 14 days postinfection, mice were euthanized by inhalation of CO2, and lungs were aseptically collected. Total RNA was isolated and subjected to RNA sequencing analysis.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Lung of PBS-treated or C. neoformans-infected mice received PBS or nor-NOHA were extracted for total RNA by using TRIzolTM and Qiagen RNeasy® Plus Mini kit. 600 ng of total RNA was used for the construction of sequencing libraries.
RNA libraries for RNA-seq were prepared using NEBNext® Ultra™ RNA library prep kit for Illumina® following the manufacturer's protocols.
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina NovaSeq 6000 |
| |
|
| Data processing |
All high-quality paired-end reads were aligned to the Mus musculus reference genome GRCm39 using Hisat2 (v 2.0.5).
NCBI BLAST v2.2.28 was used to annotate the reads based on known mouse genes with the expected value (e-value) of 1.0 x 10-10.
To estimate the abundance of the gene expression, the read numbers mapped of each gene from each transcript were counted and then normalized by fragment per kilobases per million mapped reads (FPKM) approach using HTSeq v0.6.1.
Assembly: mm10
Supplementary files format and content: tab-delimited text files include RPKM values for each Sample
|
| |
|
| Submission date |
Feb 06, 2024 |
| Last update date |
Apr 06, 2024 |
| Contact name |
Pornpimon Angkasekwinai |
| E-mail(s) |
p.akswn@gmail.com
|
| Organization name |
Thammasat University
|
| Street address |
99 Moo.18
|
| City |
Klong-luang |
| State/province |
Patumthani |
| ZIP/Postal code |
12120 |
| Country |
Thailand |
| |
|
| Platform ID |
GPL24247 |
| Series (1) |
| GSE255160 |
Arginase inhibitor reduces fungal dissemination in murine pulmonary cryptococcosis by promoting anti-cryptococcal immunity |
|
| Relations |
| BioSample |
SAMN39842193 |
| SRA |
SRX23548987 |
