Status
Public on Nov 06, 2025
Title
L_57_endo
Sample type
SRA
Source name
Lung
Characteristics
tissue: Lung
cell type: Endothelium
genotype: WT
treatment: sham_saline_endo
Treatment protocol
To model post-sepsis inflammatory memory, mice underwent cecal ligation and puncture (CLP) or sham surgery (first hit). After a recovery period, mice were challenged intranasally with either Streptococcus pneumoniae (×ばつ106 CFU) or PBS (second hit). Endothelial cells were isolated from lung and kidney tissues at defined timepoints corresponding to acute and memory phases of the response.
Growth protocol
Male C57BL/6 mice (8–12 weeks old) were housed under specific pathogen-free conditions with ad libitum access to food and water. All procedures were approved by the Institutional Animal Care and Use Committee. Mice were randomly assigned to experimental groups.
Extracted molecule
total RNA
Extraction protocol
Lung and kidney tissues were enzymatically digested into single-cell suspensions, and endothelial cells were enriched using anti-CD31 magnetic-microbeads according to the manufacturer’s protocol. CD31+ cells were lysed in Trizol reagent (Thermo Fisher Scientific), and total RNA was purified using RNeasy Micro columns (Qiagen) with on-column DNase digestion to eliminate genomic DNA contamination.
RNA-seq libraries were generated using the NEBNext Ultra II RNA Library Prep Kit for Illumina (New England Biolabs), including polyA enrichment for mRNA. Libraries were barcoded, quantified by qPCR, and sequenced on an Illumina NovaSeq 6000 using 150 bp paired-end reads.
Library strategy
RNA-Seq
Library source
transcriptomic
Library selection
cDNA
Instrument model
Illumina NovaSeq 6000
Description
Library name: lung_Sample_21
Data processing
Sequencing adapters and low-quality bases were trimmed using Trim Galore (v0.6.10). Reads were aligned to the human genome (hg38) using STAR (v2.7.10a). Gene-level counts were quantified with featureCounts (Subread v2.0.3). Differential expression was analyzed using the limma-voom pipeline in R (v4.3.2), with genes filtered by CPM >1 in at least 3 samples and adjusted p-value < 0.05.
Assembly: mm10
Supplementary files format and content: tab-delimited text files log read counts values for each Sample
Submission date
Jun 05, 2025
Last update date
Nov 06, 2025
Contact name
Ramon Bossardi Ramos
Organization name
Albany Medical College
Department
Department of Molecular and Cellular Physiology
Lab
Adam's Lab
Street address
43 New Scotland Avenue
City
Albany
State/province
Ny
ZIP/Postal code
12208
Country
USA
Series (1)
GSE299114
Endothelial Cells retain inflammatory memory through chromatin remodeling [RNA-Seq 2]
Relations
Supplementary data files not provided
Raw data are available in SRA