 |
 |
GEO help: Mouse over screen elements for information. |
|
| 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 |
| Citation missing |
Has this study been published? Please login to update or notify GEO. |
| |
| Submission date |
Mar 12, 2020 |
| Last update date |
Mar 11, 2021 |
| Contact name |
Alexander Graf |
| E-mail(s) |
graf@genzentrum.lmu.de
|
| 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)
|
|
| Relations |
| BioProject |
PRJNA612179 |
| SRA |
SRP252529 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSE146854_htseq_counts.csv.gz |
311.8 Kb |
(ftp)(http) |
CSV |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data are available on Series record |
|
|
|
|
 |
Less...
More...