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Series GSE112101 Query DataSets for GSE112101
Status Public on Jan 21, 2019
Title RNA-seq of nine primary human cell types exposed in vitro to methylprednisolone
Organism Homo sapiens
Experiment type Expression profiling by high throughput sequencing
Summary Glucocorticoids remain the most widely used class of anti-inflammatory and immunosuppressive agents. They act primarily by binding to the glucocorticoid receptor, resulting in direct and indirect effects on gene expression. The current understanding of glucocorticoid effects on transcription in human cells is based mostly on studies of cancer cell lines, immortalized cell lines, or highly mixed populations of primary cells (such as peripheral blood mononuclear cells). To advance the understanding of the transcriptome-wide effects of glucocorticoids on highly pure populations of primary human cells, we performed RNA-seq on nine such cell populations at two time points after in vitro exposure to methylprednisolone or vehicle.
Overall design Nine cell types were studied: four hematopoietic (circulating B cells, CD4+ T cells, monocytes, and neutrophils) and five non-hematopoietic (endothelial cells, fibroblasts, myoblasts, osteoblasts, and preadipocytes). Each cell type was obtained from a separate cohort of 4 unrelated healthy human donors (4 biological replicates per cell type: BR1 - BR4). Cells form each donor were independently cultured and exposed in vitro to glucocorticoid or vehicle. Non-hematopoietic cells were incubated until the early plateau phase of growth, then exposed to methylprednisolone or vehicle. Hematopoietic cells were collected from peripheral blood, purified by magnetic selection (negative selection for B cells, CD4+ T cells and neutrophils; positive selection for monocytes). Purified B cells, CD4+ T cells, and monocytes were incubated overnight, then exposed to methylprednisolone or vehicle. Purified neutrophils were cultured for 4 hours, then exposed to methylprednisolone or vehicle. Ethanol was used as a vehicle for methylprednisolone. Estimated final concentrations were 8500 mcg/L (22.7 mcM) for methylprednisolone and 0.07% (15.57 mM) for ethanol (vehicle). For each cell type, samples were collected at two time points after treatment with methylprednisolone or vehicle: 2 hours and 6 hours. Samples were collected into TRIzol reagent and frozen at -80°C prior to RNA extraction. RNA-seq data for all samples is made available in this GEO Series.
Contributor(s) Gadkari M, Kumari S, Franco LM
Citation(s) 30674564
Submission date Mar 20, 2018
Last update date Jul 20, 2020
Contact name Luis M Franco
Organization name National Institutes of Health
Department National Institute of Allergy and Infectious Diseases
Lab Laboratory of Immune System Biology
Street address 9000 Rockville Pike
City Bethesda
State/province MD
ZIP/Postal code 20892
Country USA
Platforms (2)
GPL11154 Illumina HiSeq 2000 (Homo sapiens)
GPL21290 Illumina HiSeq 3000 (Homo sapiens)
Samples (144)
GSM3057630 Mono_2H_MP_BR1
GSM3057632 Mono_2H_VH_BR1
GSM3057636 Mono_6H_MP_BR1
BioProject PRJNA439288
SRA SRP136108

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Supplementary file Size Download File type/resource
GSE112101_NormalizedReadCounts.txt.gz 26.0 Mb (ftp)(http) TXT
GSE112101_RawReadCounts.txt.gz 5.6 Mb (ftp)(http) TXT
GSE112101_differential_expression_results.xlsx 37.9 Mb (ftp)(http) XLSX
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Raw data are available in SRA
Processed data are available on Series record

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