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| Status |
Public on Dec 02, 2023 |
| Title |
M-2-2 |
| Sample type |
SRA |
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| Source name |
Bronchoalveolar lavage
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| Organism |
Mus musculus |
| Characteristics |
strain: MSDC
treatment: MSDC
tissue: lung
cell type: Alveolar macrophages
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| 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.
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| 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).
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| 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.
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| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 4000 |
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| 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 ...
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| Submission date |
Oct 25, 2022 |
| Last update date |
Dec 02, 2023 |
| Contact name |
Xiaoqin Wei |
| E-mail(s) |
hqt8dz@virginia.edu
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| Phone |
15715238364
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| Organization name |
University of Virginia
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| Street address |
2512 Fontaine Ave
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| City |
Charlottesville |
| State/province |
Virginia |
| ZIP/Postal code |
22908 |
| Country |
USA |
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| Platform ID |
GPL21103 |
| Series (1) |
| GSE216564 |
Characterization of in vitro cultured alveolar macrophages (AM) transcriptomes |
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| Supplementary data files not provided |
| Raw data not provided for this record |
| Processed data are available on Series record |
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