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| Status |
Public on Jul 09, 2019 |
| Title |
LPS rep2 |
| Sample type |
SRA |
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| Source name |
Macrophage
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| Organism |
Homo sapiens |
| Characteristics |
cell type: Macrophage
treatment: LPS
treatment time: 3h
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| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA was extracted using Trizol and Rneasy mini kit with an additional purification step by on-column DNAse treatment using Rnase-free Dnase Kit (Qiagen)
RNA libraries were prepared for sequencing using NEBNext Ultra II Directional RNA Library Prep kit for Illumina
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| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 2500 |
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| Description |
TDC_10
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| Data processing |
Illumina CASAVA-1.8.4 software used for basecalling.
Sequencing adapters were removed using Trimmomatic (v.0.36) and the reads quality was checked using FastQC (v.0.11.2) before and after trimming. Reads were aligned to the human genome (GRCh38.primary_assembly.genome.fa; annotation: gencode.v25.annotation.gtf) using tophat2 package (v.2.1.0: -b2-sensitive,--library-type fr-firststrand). Mapping quality, read distribution, gene body coverage, GC content and rRNA contamination, were checked using picard (v.2.6.0) software.
Gene level read counts were computed using HT-Seq-count (v.0.6.1, annotation: gencode.v25.annotation.gtf)1 with strict "-m intersection-strict” mode. Genes with less than 10 aligned reads across all samples were filtered out as lowly expressed genes.
Differential gene expression analysis between groups was performed using DESeq2 (v.1.14.1)4 and significantly differentially expressed genes were reported using fold-change at 1.5 times and below 1 % Benjamini-Hochberg (BH) adjusted p-value.
In order to visualize the similarities between samples, unsupervised hierarchical clustering and principal component analysis (PCA) were performed using pcaExplorer (v.2.6.0, https://github.com/federicomarini/pcaExplorer) and pheatmap (v 1.0.10, https://CRAN.R-project.org/package=pheatmap) packages respectively. Volcano plots of differentially expressed genes were generated using ggplot2 (v.3.0.0, https://cran.r-project.org/web/packages/ggplot2/index.html) package.
Genome_build: GRCh38.primary_assembly.genome.fa; annotation: gencode.v25.annotation.gtf)
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| Submission date |
Mar 26, 2019 |
| Last update date |
Sep 13, 2023 |
| Contact name |
Norzawani Binti Buang |
| E-mail(s) |
n.buang13@imperial.ac.uk
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| Phone |
07716497826
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| Organization name |
Imperial College London
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| Street address |
9N15 Commonwealth Buidling, Ducane Road
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| City |
London, United Kingdom |
| State/province |
London |
| ZIP/Postal code |
W12 0NN |
| Country |
United Kingdom |
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| Platform ID |
GPL16791 |
| Series (1) |
| GSE128885 |
RNA sequencing of human macrophages treated with iron chelator deferiprone (DEF), with and without lipopolysaccharide (LPS) |
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| Relations |
| BioSample |
SAMN11258682 |
| SRA |
SRX5577114 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSM3687983_TDC_10_total.count.txt.gz |
233.2 Kb |
(ftp)(http) |
TXT |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data provided as supplementary file |
| Processed data are available on Series record |
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