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| Status |
Public on Aug 23, 2021 |
| Title |
RNAseq2_BMDM_Dex_IFNg_LPS_rep1 [L_g_D_1] |
| Sample type |
SRA |
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| Source name |
RNAseq2_BMDM_Dex_IFNg_LPS
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| Organism |
Mus musculus |
| Characteristics |
strain: C57BL/6J
cell type: bone marrow-derived macrophage (BMDM)
treatment: Dex_IFNg_LPS
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| Treatment protocol |
For activation of macrophages, cells were treated with vehicle, Dex (1uM), iBRD9 (3 or 10uM), dBRD9 (250nM) or combination for overnight, followed by stimulation of LPS (100ng/ml, Sigma) for 3 hours, before harvested for RNA-seq.
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| Growth protocol |
BMDMs were isolated similarly as described before. Briefly, bone marrow from 6-12 weeks old male animals. After lysis with AKC lysis buffer, cells were plated in petri dishes, cultured with media containing RPMI, 20% FBS, 30% L-929 conditional medium, and 1% penicillin/streptomycin or anti-anti. Macrophages were digested with versine and plated with macrophage serum free medium.
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| Extracted molecule |
total RNA |
| Extraction protocol |
libraries were prepared for sequencing using standard Illumina protocols.
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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 |
Raw data (raw reads) of FASTQ format were firstly processed through fastp. In this step, clean data (clean reads) were obtained by removing reads containing adapter and poly-N sequences and reads with low quality from raw data.
At the same time, Q20, Q30 and GC content of the clean data were calculated. All the downstream analyses were based on the clean data with high quality. Paired-end clean reads were aligned to the reference genome using the Spliced Transcripts Alignment to a Reference (STAR) software.
FPKM of each gene was calculated based on the length of the gene and reads count mapped to this gene. Differential expression analysis between two conditions/groups (three biological replicates per condition) was performed using DESeq2 R package. DESeq2 provides statistical routines for determining differential expression in digital gene expression data using a model based on the negative binomial distribution. The resulting P values were adjusted using the Benjamini and Hochberg’s approach for controlling the False Discovery Rate (FDR). Genes with an adjusted P value < 0.05 and fold change >1.5 found by DESeq2 were assigned as differentially expressed.
Genome_build: mm10
Supplementary_files_format_and_content: XLS
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| Submission date |
May 26, 2021 |
| Last update date |
Aug 23, 2021 |
| Contact name |
Zong Wei |
| E-mail(s) |
[email protected]
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| Organization name |
Mayo Clinic
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| Lab |
WEI LAB
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| Street address |
13400 E Shea Blvd
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| City |
SCOTTSDALE |
| State/province |
Arizona |
| ZIP/Postal code |
85259 |
| Country |
USA |
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| Platform ID |
GPL21103 |
| Series (2) |
| GSE175584 |
Bromodomain containing 9 (BRD9) regulates macrophage inflammatory responses and modulates glucocorticoids receptor activity [RNA-seq] |
| GSE175585 |
Bromodomain containing 9 (BRD9) regulates macrophage inflammatory responses and modulates glucocorticoids receptor activity. |
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| Relations |
| BioSample |
SAMN19355517 |
| SRA |
SRX11001709 |
| Supplementary data files not provided |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data are available on Series record |
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