cell culture 852 human embryonic kidney hek 293ft cells  (ATCC)

Journal: Nature

Article Title: Epigenetic memory of colitis promotes tumour growth

doi: 10.1038/s41586-026-10258-4

Figure Lengend Snippet: a, Fluorescent in situ hybridization against GFP for clonal barcode transcripts in HEK293T cells. Top, cells infected with original LARRY barcode from Weinreb et al. Bottom, cells infected with LARRY barcode modified by addition of mU1 hairpin sequence. Scale bar 50 μm. Representative of n = 100 cells across 2 independent experiments. b, Schematic detailing molecular process of capturing clonal barcodes and computational workflow for assigning cells to clones. c, HNF4/PPAR motif accessibility amongst the 50 largest clones by cell number. Each violin plot represents distribution of motif scores for an individual clone and point represents median values per clone. d, Framework for computing clonal variance and identifying clonal features. e, Motif accessibility relative to position in the colon. The X-axis represents segment of the colon, with segment 1 being most proximal and segment 6 being most distal. The Y-axis shows change in motif accessibility of a given segment relative to segment 1. f, Accessibility of all TF motif families relative to position in the colon. Each row represents a TF motif family and color indicates change in motif accessibility relative to segment 1. g, Expression stemness ( Lgr5 , Lrig1 ) and differentiation ( Car1 ) markers in relation to HNF4/PPAR motif score. h, Downsampling analysis of permutation-based clonal heritability. Clones were randomly sampled to the number indicated on the x-axis and permutation-based testing was performed identically to the complete dataset. The total number of motif families identified to have lower clonal variance as compared to random (FDR < 0.05) for each clone number is shown on the y-axis. i, Linear mixed model of random effects from exposure to colitis and clonal identity. j, Variance explained by clonal identity from the linear mixed model. k, Comparison of variance explained by clonal identity and exposure to colitis for all TF motif families. l, Left, variance explained by clonal identity and exposure to colitis for top TF motif families. Right, variance attributed to each factor following randomization of clonal identities within colitis or control conditions. m, Comparison of clonality identified by permutation and linear mixed model. The X-axis shows -log10(FDR) from the permutation method (Fig. ) and the Y-axis shows percent variance attributed to clonal identity in the linear mixed model (panel j). Panels created in BioRender: e , Nagaraja, S. https://biorender.com/jqhj3wt (2026); i , Nagaraja, S. https://biorender.com/4mut8sd (2026).

Article Snippet: Human embryonic kidney 293T (HEK293T) cells (American Type Culture Collection (ATCC), CRL-3216; authenticated by short tandem repeat profiling and tested for mycoplasma by ATCC) were grown in DMEM (Thermo, 11965-092) with 10% fetal bovine serum (FBS) and 1% penicillin–streptomycin.

Techniques: In Situ Hybridization, Infection, Modification, Sequencing, Clone Assay, Expressing, Comparison, Control

Journal: Journal of Virology

Article Title: ALDH1L1 suppresses the replication of porcine epidemic diarrhea virus by degrading viral nucleocapsid and envelope proteins

doi: 10.1128/jvi.01933-25

Figure Lengend Snippet: ALDH1L1 interacts with and degrades PEDV N and E proteins via the selective autophagy pathway. ( A and B ) HEK 293T cells were transfected with plasmids coding HA-N or HA-E and Flag-ALDH1L1. Co-IP assay was performed using anti-Flag-bound beads. ( C and D ) After inducing Flag-ALDH1L1 and GST-N or GST-E expression in the BL21(DE3) bacterial strain, the associations of ALDH1L1 with N or E proteins were analyzed via the GST pull-down assay. ( E and F ) After transfection with HA-N or HA-E and Flag-ALDH1L1, HeLa cells were labeled with antibodies and nuclear DAPI for confocal immunofluorescence microscopy. Scale bars = 100 µm. ( G and H ) After transfecting HEK 293T cells with varying concentrations of Flag-ALDH1L1, HA-N, or HA-E, western blotting was performed to assess N and E protein expression. ( I and J ) HEK 293T cells were transfected with plasmids coding the Flag-ALDH1L1 plasmid and HA-N or HA-E, followed by treatment with BafA1 (50 µM), CQ (50 µM), MG132 (5 µM), or 3-MA (1 mM) for 10 h. The resulting cellular lysates were subjected to western blotting.

Article Snippet: Dulbecco’s modified Eagle’s medium (Sigma-Aldrich, D6429) supplemented with 10% fetal bovine serum (Gibco, 10099141) was used to culture human embryonic kidney HEK 293T cells (ATCC, CRL-11268) and African green monkey kidney Vero cells (ATCC, CCL-81).

Techniques: Transfection, Co-Immunoprecipitation Assay, Expressing, Pull Down Assay, Labeling, Immunofluorescence, Microscopy, Western Blot, Plasmid Preparation

Journal: Journal of Virology

Article Title: ALDH1L1 suppresses the replication of porcine epidemic diarrhea virus by degrading viral nucleocapsid and envelope proteins

doi: 10.1128/jvi.01933-25

Figure Lengend Snippet: ALDH1L1 inhibits PEDV replication via the E3 ubiquitin ligase STUB1. ( A ) After HEK 293T cells were cotransfected with plasmids encoding HA-STUB1 and Flag-ALDH1L1, the Co-IP assay was performed using anti-Flag-bound beads. ( B ) After HEK 293T cells were transfected with plasmids coding Flag-ALDH1L1, Co-IP assays were performed using an anti-Flag antibody. ( C ) After inducing GST-STUB1 and ALDH1L1 expression in the BL21(DE3) strain, the interaction between ALDH1L1 and STUB1 was examined via the GST pull-down assay. ( D ) After cotransfecting HeLa cells with Flag-ALDH1L1 and STUB1-HA for 24 h via incubation with an anti-Flag Mab, ALDH1L1 and STUB1 colocalization was confirmed via confocal immunofluorescence microscopy. Scale bars = 100 µm. ( E and F ) After cotransfection with Myc-ALDH1L1, HA-Ub, HA-STUB1, and Flag-N, or Flag-E, HEK 293T cells were treated with CQ and collected. The ubiquitinated N and E proteins were subjected to western blotting after immunoprecipitation with an anti-Flag antibody. ( G and H ) After cotransfecting HEK 293T cells with siRNAs (negative control or STUBA siRNA) and HA-N or HA-E and Flag-ALDH1L1-coding plasmids, western blotting was performed with an anti-HA antibody.

Article Snippet: Dulbecco’s modified Eagle’s medium (Sigma-Aldrich, D6429) supplemented with 10% fetal bovine serum (Gibco, 10099141) was used to culture human embryonic kidney HEK 293T cells (ATCC, CRL-11268) and African green monkey kidney Vero cells (ATCC, CCL-81).

Techniques: Ubiquitin Proteomics, Co-Immunoprecipitation Assay, Transfection, Expressing, Pull Down Assay, Incubation, Immunofluorescence, Microscopy, Cotransfection, Western Blot, Immunoprecipitation, Negative Control

Journal: Journal of Virology

Article Title: ALDH1L1 suppresses the replication of porcine epidemic diarrhea virus by degrading viral nucleocapsid and envelope proteins

doi: 10.1128/jvi.01933-25

Figure Lengend Snippet: ALDH1L1 suppresses PEDV replication via the cargo receptor TOLLIP. ( A ) After cotransfecting HEK 293T cells with plasmids coding HA-TOLLIP and Flag-ALDH1L1, a Co-IP assay was performed with anti-Flag-bound beads. ( B ) After transfecting HEK 293T cells with plasmids encoding Flag-ALDH1L1, Co-IP assays were performed using an anti-Flag antibody. ( C ) After inducing GST-TOLLIP and ALDH1L1 expression in the BL21(DE3) strain, the interaction between ALDH1L1 and TOLLIP was examined via the GST pull-down assay. ( D ) HeLa cells were transfected with plasmids coding Flag-ALDH1L1 and HA-TOLLIP. Then, the cells were incubated with specific antibodies and visualized under a confocal immunofluorescence microscope. Scale: 100 µm. ( E and F ) After cotransfecting HEK 293T cells with siRNAs (negative control or TOLLIP siRNA) and HA-N or HA-E and Flag-ALDH1L1-coding plasmids, western blotting was performed using an anti-HA antibody.

Article Snippet: Dulbecco’s modified Eagle’s medium (Sigma-Aldrich, D6429) supplemented with 10% fetal bovine serum (Gibco, 10099141) was used to culture human embryonic kidney HEK 293T cells (ATCC, CRL-11268) and African green monkey kidney Vero cells (ATCC, CCL-81).

Techniques: Co-Immunoprecipitation Assay, Expressing, Pull Down Assay, Transfection, Incubation, Immunofluorescence, Microscopy, Negative Control, Western Blot