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Splenic T cells were isolated by negative selection from wt, MKK3+/−, or MKK3−/− mice, as described [40].
CD4+ lymphocytes were isolated by negative selection from PBMC, more than 95% of isolated cells were CD4+ as tested by flow cytometry.
CD25− fraction (effector population) was isolated by negative selection from the remaining CD4+CD45RO+ fraction with the addition of 106/50µl cells of CD25+ positive selection Dynabeads at room temperature for 40 minutes.
DN γδ T cells were purified by negative selection from the LNs of WT γδTCR Tg, Lck+/− γδTCR Tg and Fyn+/− γδTCR Tg mice using the MACS magnetic bead separation system (Miltenyi Biotec, Auburn, CA, USA).
NK cells were isolated by negative selection from PBMCs depleted of monocytes using a depletion cocktail of antibodies directed to CD3, CD4, CD14, CD19, CD20, CD36, CD123, CD66b, Glycophorin A (StemCell Technologies).
ECM-treated and ECM-untreated DC were loaded with CMV protein for 3 h before co-culturing with autologous memory T-cells, separated by negative selection from the whole T-cell fraction of PBMCs using a Pan T-cell Kit and CD45RO beads (Miltenyi Biotec).
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CD19+ cells were obtained by negative selection using reagents from StemCell Technologies (Vancouver BC).
Although we do not have power to classify 10 kb windows as completely unconstrained by negative selection, the results from table 1 imply that our popCons elements probably contain a substantially greater density of selected sites than popUncons on average.
Naïve T cells and total CD4+ T cells were isolated from PBMCs by negative selection using magnetic beads based kits from Miltenyi Biotec.
B cell-enriched population was obtained from PBMCs by negative selection using human B cell Isolation kit from Miltenyi Biotec (Bologna, Italy).
On the day of assay (the last day of activation of CD8 T cells), CD8 T cells were separated from Treg cells by negative selection using the mouse Dynabeads CD4 (L3T4) from Invitrogen.
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