u/Subject_Plankton_328

Hello, I work extensively with ENCODE data (if you're not familiar with this, it's a big consortium that produces and analyzes various aspects of human and mouse genomes and genetic regulation, broadly speaking), and I am curious about how some of the T cell samples I work with were activated, since it doesn't exactly align with the canonical three-part activation I learned about in my undergraduate immunology class.

Basically, I am looking at differences in genome organization between resting and activated T cells, but the treatment protocols continue to confuse me. Here is the description from the lab that did the actual activation:

"CD4+ and CD8+ T cells and their subsets were left resting in culture or activated using anti-CD3 and anti-CD28 (aCD3/aCD28) coated beads (Invitrogen cat# 11132D) (1 bead:2 cells ratio) and cultured in complete RPMI 1640 at 10M/6ml/well in 6 well-plate. Resting cells and 90% of activated T cells were collected on day 2 (36 hours) and beads were removed using Dynal magnet. The rest of activated cells was expanded in rhIL-2 (10 ng/ml, R&D Systems cat# 10453-IL-100) containing media for 5 to 6 more days and collected on day 7 or day 8 post activation. Activation of T cells was confirmed by the upregulation of CD25 and CD69 surface expression analyzed by flow cytometry. For differentiation into different T helper (Th) subsets, Naïve CD4+ (sorted CD45RO- CCR7+) T cells were activated with anti-CD3 and anti-CD28 beads in the presence of the following polarizing cytokine and blocking antibody combinations: Th0, medium only, Th1, human IL-12 (R&D Systems cat# 219-IL-025; 30 ng/ml) and neutralizing anti-IL-4 Antibody (R&D Systems cat# AF-204-NA; 1 μg/ml), and Th2, human IL-4 (R&D Systems cat# 204-IL-020; 100 ng/ml) and neutralizing anti-IFN-γ Antibody (R&D Systems cat# MAB285-100; 5 μg/ml). Cells were cultured and expanded in rhIL-2 (10 ng/ml, R&D Systems cat# 10453-IL-100) containing media for 2 weeks. On day 13 after activation, some of the cells were reactivated with aCD3/aCD28 beads (at 1 bead:3 cells ratio) for another 24 hours."

Can anyone tell me if this is standard procedure for in vitro T cell stimulation that closely mimics in vivo activation, or is there something off here that I need to be aware of?

Thanks in advance for reading this and for your help!!

How bad is it if I scheduled my UTMB interview and orientation day for a set time, then scheduled another interview for the same day as the orientation without realizing? I have exchanged a few emails with them, and I am trying to be as respectful as possible, but is it doomed? Obviously this is completely my fault lol but I’m curious if anyone else has had this happen to them and what was their outcome.

EDIT: they were able to move it!!

Hey, hopefully some of the people here are prospective students or employees that are still looking for housing near the UTMB Galveston campus. I (21M) am an incoming research assistant that will be spending a gap year here from about June 1st 2026 until the same day in 2027. Unfortunately since I’m not an incoming graduate school student Im not on the facebook housing group, but if anyone is in a similar position or looking to split housing please reach out to me!