Dataset: Transcription profilin by array of human CD34+ hematopoietic progenitor cells grown under different conditions

Gene transfer vectors based on gamma-retroviruses target actively transcribing genes indicating that the cellular gene expression profile can be predictive of their integration pattern. Therefore, different culture conditions leading to different transcriptional activity may translate into differences in the profile of targeted genes in cells transduced with these vectors. Recent data from two gene therapy trials for SCID-X1 conducted in France and the UK suggested that small differences between in vitro stimulation conditions could explain the disparity in the frequency of common integrations sites observed in the two studies. We set out to compare the transcriptional activity of human CD34+ bone marrow-derived cells cultured under the French (S1) or British (S2) culture conditions. RNA was extracted from human CD34+ bone marrow-derived cells from 3 donors stimulated under the French (S1) conditions (X-vivo 10, 4% fetal calf serum, 300 ng/ml stem cell factor [SCF], 100 ng/ml thrombopoietin [TPO], 60 ng/ml interleukin-3 [IL3], and 300 ng/ml Flt3 ligand [FL]) and under the British (S2) conditions (X-vivo 10, 1% human serum albumin, 300 ng/ml SCF, 100 ng/ml TPO, 20 ng/ml IL3, and 300 ng/ml FL). Extracted RNA was amplified with random hexamer primer reverse transcription strategy. Lastly, amplified RNA was labeled and hybridized to HG U133 Plus 2.0 Affymetrix microarrays. Four time points during cytokine stimulation were analyzed, corresponding to 0 hr and three transduction time points in the French and British SCID-X1 gene therapy clinical trials (48 h, 72 h, and 96 h). Samples are referred to as donor, stimulation condition, and time point (e.g., Don 1 S1-48 for donor 1 of 3, S1 stimulation conditions, and 48 h after stimulation was begun).

Species:

human

Samples:

21

Source:

E-GEOD-20505

Updated:

Dec.12, 2014

Registered:

Sep.15, 2014