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Sample GSM8065011 Query DataSets for GSM8065011
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

Supplementary file Size Download File type/resource
GSM8065011_Processed_data_file_PBS1.txt.gz 2.1 Mb (ftp)(http) TXT
SRA Run SelectorHelp
Raw data are available in SRA

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