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Sample GSM6679252 Query DataSets for GSM6679252
Status Public on Dec 02, 2023
Title D-2-1
Sample type SRA
 
Source name Bronchoalveolar lavage
Organism Mus musculus
Characteristics strain: DMSO
treatment: DMSO
tissue: lung
cell type: Alveolar macrophages
Treatment protocol AMs were pre-treated with DMSO (vehicle) or MSDC (10 μM) for two hours, then, cells were stimulated with or without Poly IC (5μg/mL) for 24 hours. Then, the cells were havested for RNA-seq.
Growth protocol AMs were obtained from bronchoalveolar lavage of mice and purified by adherence for 2 h in complete medium (RPMI-1640, 10% FBS, 1% Pen/Strep/glutamate) at 37 ̊C and 5% CO2. The non-adherent cells were washed off with warm PBS. The remaining adherent cells were cultured in complete medium supplemented with 10 ng/ml recombinant murine granulocyte macrophage CSF (GM-CSF).
Extracted molecule total RNA
Extraction protocol Total RNA from in vitro cultured AMs was extracted using RNeasy Plus Mini Kit, and RNA quality was determined (RIN>7) via Agilent Bioanalyzer
Libraries were prepared according to Illumina's instructions accompanying the RNA Sample Kit.
 
Library strategy RNA-Seq
Library source transcriptomic
Library selection cDNA
Instrument model Illumina HiSeq 4000
 
Data processing Paired-end libraries were sequenced on an Illumina HiSeq 4000 following Illumina’s standard protocol using the Illumina cBot and HiSeq 3000/4000 PE Cluster Kit. Base-calling was performed using Illumina’s RTA software (version 2.5.2). Paired-end RNA-seq reads were aligned to the mouse reference genome (GRCm38/mm10) using RNA-seq spliced read mapper Tophat2 (v2.1.1).
Paired-end RNA-seq reads were aligned to the mouse reference genome (GRCm38/mm10) using Bowtie (v2.3.4). Pre- and post-alignment quality controls, gene level raw read count and normalized read count (i.e. FPKM) were performed using RSeQC package (v2.3.6) with NCBI mouse RefSeq gene model.
Differential expression for each gene between various groups was identified by Cuffdiff. For functional analysis, GSEA was used to identify enriched gene sets, from the hallmark and C5 databases of MSigDB, having up-regulated and down-regulated genes, using a weighted enrichment statistic and a log2 ratio metric for ranking genes.
Assembly: mm10
Supplementary files format and content: csv file include FPKM values for each Sample ...
 
Submission date Oct 25, 2022
Last update date Dec 02, 2023
Contact name Xiaoqin Wei
E-mail(s) hqt8dz@virginia.edu
Phone 15715238364
Organization name University of Virginia
Street address 2512 Fontaine Ave
City Charlottesville
State/province Virginia
ZIP/Postal code 22908
Country USA
 
Platform ID GPL21103
Series (1)
GSE216564 Characterization of in vitro cultured alveolar macrophages (AM) transcriptomes

Supplementary data files not provided
Raw data not provided for this record
Processed data are available on Series record

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