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Series GSE146854 Query DataSets for GSE146854
Status Public on Mar 11, 2021
Title Transcriptome analysis of activated CD4+ T cells treated either with sodium butyrate or bufexamac
Organism Homo sapiens
Experiment type Expression profiling by high throughput sequencing
Summary Sodium butyrate and bufexamac treatment of activated CD4+ T cells impairs de novo HIV-1 infection. RNAseq was used to obtain information about the cellular changes upon treatment, which could explain the observed effects on HIV-1 infection
Overall design CD4 T cells were isolated from PBMCs using Easy-SepTM Rosette Human CD4+ T cell enrichment kit (Stemcell Technologies, Canada). Isolated cells were activated with IL-2 and PHA for 5-7 days according to standard protocols. To minimize donor effects, activated T cells from four donors were pooled and activated CD4+ T cell-pools were treated either with 1.95 mM sodium butyrate or 0.04 mM bufexamac and cultured for 48 h. Untreated T cell-pools served as control. Subsequently, cells were harvested, washed with PBS, and RNA was isolated from trizol lysates of cells using Direct-zol RNA Miniprep Kit (Zymo Research) following manufacturer’s instructions. Isolated RNA was additionally purified using Agencourt RNAClean XP beads (Beckman Coulter) following manufacturer’s instructions. In total 3 independent samples of untreated, sodium butyrate treated , and bufexamac treated cells were generated. After quantification (Nanodrop), the RNA was quality controlled using a Bioanalyzer (Agilent Technologies). Good quality RNA (RIN > 7) was used to generate sequencing libraries by using 500 ng total RNA in a Sense mRNA Seq Libarary Prep Kit V2 for Illumina platforms (Lexogen) following manufacture’s instructions. Libraries were quantified and subsequently sequenced on an Illumina HiSeq 1500 (sequencing mode: 100 nt, single-end). The sequencing data was preprocessed on a Galaxy server (hosted by LAFUGA, Gene Center, Munich). After demultiplexing, the data was trimmed according to Lexogen. The output was mapped to the human genome (hg19) using STAR (v. 2.5.2b-0). Abundant reads were further analyzed using HTSeq-count (v. 1.0.0) and a differential gene expression analysis was performed using DESeq (v. 1.0.19) setting the FDR < 0.01.
Contributor(s) Chen L, Zutz A, Phillippou-Massier J, Liebner T, Keppler OT, Choudhary C, Blum H, Schölz C
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Submission date Mar 12, 2020
Last update date Mar 11, 2021
Contact name Alexander Graf
Organization name Ludwig-Maximilians-Universität München
Department Gene Center Munich
Street address Feodor-Lynen-Str. 25
City Munich
ZIP/Postal code 81377
Country Germany
Platforms (1)
GPL18460 Illumina HiSeq 1500 (Homo sapiens)
Samples (9)
GSM4407898 Control 1
GSM4407899 Control 2
GSM4407900 Control 3
BioProject PRJNA612179
SRA SRP252529

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Supplementary file Size Download File type/resource
GSE146854_htseq_counts.csv.gz 311.8 Kb (ftp)(http) CSV
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Raw data are available in SRA
Processed data are available on Series record

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