Journal: eLife

Article Title: Interplay between PML NBs and HIRA for H3.3 dynamics following type I interferon stimulus

doi: 10.7554/eLife.80156

Figure Lengend Snippet:

Article Snippet: Human BJ primary foreskin fibroblasts (ATCC, CRL-2522), human IMR90 fetal lung fibroblasts (ATCC, CCL-186), human HEK 293T embryonic kidney cells (Intercell, AG) and mouse MEFs embryonic fibroblasts Pml +/+ or Pml -/- (from Dr. Lallemand-Breitenbach, and whose cell identity was authenticated by STR profiling) were cultivated in DMEM medium (Sigma-Aldrich, D6429) containing 10% of fetal calf serum (FCS) (Sigma-Aldrich, F7524), 1% of penicillin/streptomycin (Sigma-Aldrich, P4458), at 37 °C under 5% CO2 and humid atmosphere.

Techniques: Transduction, Recombinant, Plasmid Preparation, Clone Assay, Mutagenesis, Sequencing, Quantitative RT-PCR, Concentration Assay, In Situ, Software, ChIP-sequencing

Journal: BMC Medical Genomics

Article Title: VNTR polymorphism in the breakpoint region of ABL1 and susceptibility to bladder cancer

doi: 10.1186/s12920-021-00968-1

Figure Lengend Snippet: Functional analysis of the VNTRs within ABL1 -MS1 in luciferase reporter vector promoter region. a ABL1 promoter vector (p2000) and four promoter vectors in which four different lengths of ABL1 -MS1 (TR13–TR16) were inserted were used. The ABL1 promoter region is indicated by diagonal squares, and the luciferase gene is indicated by gray squares. Four different lengths of ABL1 -MS1 were inserted after the luciferase gene and are indicated by black squares. b The above five different types of promoter vectors were transfected into 293 T and UC3 cells. ABL1 promoter activity was measured by luciferase assay

Article Snippet: The following human cell lines were tested for the effect of ABL1 -MS1 on ABL1 expression: 293 T (human embryonic kidney cell line obtained from the Korean Cell Line Bank; KCLB, Seoul, Korea) and UM-UC3 (bladder cancer cell line).

Techniques: Functional Assay, Luciferase, Plasmid Preparation, Transfection, Activity Assay

Journal: BMC Medical Genomics

Article Title: VNTR polymorphism in the breakpoint region of ABL1 and susceptibility to bladder cancer

doi: 10.1186/s12920-021-00968-1

Figure Lengend Snippet: VNTR analysis of ABL1 -breakpoint cluster region. a Schematic of the VNTR region of ABL1 . 11 exons are marked as black boxes and 10 introns as white boxes. One VNTR region was identified in the ABL1 -breakpoint cluster region, named MS1, and marked with an asterisk. b The location of ABL1 -MS1, the size of the repeating unit, and the consensus sequence were confirmed from the genome information of NCBI

Article Snippet: The following human cell lines were tested for the effect of ABL1 -MS1 on ABL1 expression: 293 T (human embryonic kidney cell line obtained from the Korean Cell Line Bank; KCLB, Seoul, Korea) and UM-UC3 (bladder cancer cell line).

Techniques: Sequencing

Journal: BMC Medical Genomics

Article Title: VNTR polymorphism in the breakpoint region of ABL1 and susceptibility to bladder cancer

doi: 10.1186/s12920-021-00968-1

Figure Lengend Snippet: Allelic type patterns of ABL1 -MS1 in cancer-free male controls and bladder cancer patients. a Haplotype patterns in cancer-free controls and cases with bladder cancer. The left panel is the haplotype pattern for ABL1 -MS1 region from control samples. Three genotypes were identified consisting of two different ABL1 -MS1 alleles. The right panel is the ABL1 -MS1 haplotype pattern seen in bladder cancer patients, showing five genotypes consisting of four different ABL1 -MS1 alleles. The first and last lanes correspond to a 100-bp (M1; Invitrogen Co., CA, USA) and a 1-kb size marker (M2; Invitrogen Co.). b Frequency of genotypes between controls and bladder cancer cases. N corresponds to the total number of samples tested for the allele of ABL1 -MS1. C corresponds to the common alleles (13TR, 15TR) and indicates alleles with a frequency of 1% or more. Rare alleles (R) with a frequency of less than 1% correspond to 14TR and 16TR. * Statistically significant ( P < 0.05)

Article Snippet: The following human cell lines were tested for the effect of ABL1 -MS1 on ABL1 expression: 293 T (human embryonic kidney cell line obtained from the Korean Cell Line Bank; KCLB, Seoul, Korea) and UM-UC3 (bladder cancer cell line).

Techniques: Control, Marker

Journal: BMC Medical Genomics

Article Title: VNTR polymorphism in the breakpoint region of ABL1 and susceptibility to bladder cancer

doi: 10.1186/s12920-021-00968-1

Figure Lengend Snippet: Comparison of allelic frequency of ABL1 -MS1 between controls and bladder cancer

Article Snippet: The following human cell lines were tested for the effect of ABL1 -MS1 on ABL1 expression: 293 T (human embryonic kidney cell line obtained from the Korean Cell Line Bank; KCLB, Seoul, Korea) and UM-UC3 (bladder cancer cell line).

Techniques: Comparison

Journal: BMC Medical Genomics

Article Title: VNTR polymorphism in the breakpoint region of ABL1 and susceptibility to bladder cancer

doi: 10.1186/s12920-021-00968-1

Figure Lengend Snippet: Meiotic segregation of ABL1 -MS1. a Meiotic inheritance of the ABL1 -MS1 in a third-generation family. ABL1 -MS1 were analyzed for minisatellite length in genomic DNA from family members. The pedigree demonstrates the relationship between family groups used in this study: first-generation (lanes 1 and 2, grandfather and grandmother, respectively); second-generation (lanes 3 and 4, father and mother); and third-generation (lanes 5 and 6, children from parents 3 and 4. b Meiotic inheritance the ABL1 -MS1 in three of second-generation. The first-generation is denoted as 1 and 2 (mother and father). The second-generation was shown as 3 and 4, and 5 (children). M corresponds to the size marker

Article Snippet: The following human cell lines were tested for the effect of ABL1 -MS1 on ABL1 expression: 293 T (human embryonic kidney cell line obtained from the Korean Cell Line Bank; KCLB, Seoul, Korea) and UM-UC3 (bladder cancer cell line).

Techniques: Marker

Journal: BMC Medical Genomics

Article Title: VNTR polymorphism in the breakpoint region of ABL1 and susceptibility to bladder cancer

doi: 10.1186/s12920-021-00968-1

Figure Lengend Snippet: Composition of repeats unit of ABL1 -MS1 alleles

Article Snippet: The following human cell lines were tested for the effect of ABL1 -MS1 on ABL1 expression: 293 T (human embryonic kidney cell line obtained from the Korean Cell Line Bank; KCLB, Seoul, Korea) and UM-UC3 (bladder cancer cell line).

Techniques:

Journal: PLoS ONE

Article Title: Design and Evaluation of Optimized Artificial HIV-1 Poly-T Cell-Epitope Immunogens

doi: 10.1371/journal.pone.0116412

Figure Lengend Snippet: (A) 2.5% agarose gel electrophoresis of RT-PCR products derived from isolated mRNA after 293T cells transfection with obtained plasmids. Lanes 1–3, PCR fragments of 435 bp correspond to P1, P2, and P3 plasmids; Lanes 4–6, PCR fragments of 624 bp correspond to P1, P2, and P3 plasmids; K, negative control sample (total mRNA extracted from transfected cells); M, 100bp DNA Ladder (SibEnzyme, Russia). (B) Western blot analysis of expression products of genes encoding TCI-N, TCI-N2, and TCI-N3 proteins in transfected 293T cells. Lanes P1, P2, P3 are lysates of 293T cell transfected with P1, P2, P3, respectively; lane К represents lysates of 293T cells transfected with vector plasmid pcDNA3.1. The membrane containing the cell-associated fractions was also probed with аnti-beta аctin antibody to control for equal loading of the samples. (C) Flow cytometry analyses of expression products of target genes after transfection of 293T cells with P1, P2, and P3 plasmids. Histogram overlays of target proteins stained with FITC-labeled 29F2 monoclonal antibodies (green peak, TCI-N; blue peak, TCI-N2; and yellow peak, TCI-N3 polyepitope protein expression). Negative control (read peak) represents 293T cells transfected with vector plasmid pcDNA3.1.

Article Snippet: 293T (human embryonic kidney cell line) cells were cultured in RPMI (Biolot, Russia) supplemented with 10% fetal bovine serum (FBS, Gibco-BRL, Rockville, MD).

Techniques: Agarose Gel Electrophoresis, Reverse Transcription Polymerase Chain Reaction, Derivative Assay, Isolation, Transfection, Negative Control, Western Blot, Expressing, Plasmid Preparation, Membrane, Control, Flow Cytometry, Staining, Labeling, Bioprocessing

Journal: The Journal of Biological Chemistry

Article Title: Modeling protease-sensitive human pancreatic lipase mutations in the mouse ortholog

doi: 10.1016/j.jbc.2024.107763

Figure Lengend Snippet: Secretion of mouse PNLIP variants. A , PNLIP protein levels in the conditioned media of transiently transfected HEK 293T cells were analyzed by reducing SDS-PAGE and Coomassie staining ( upper panel). PNLIP protein levels in the total cell lysates were determined by SDS-PAGE and western blotting ( lower panel). The levels of GAPDH were also assessed as controls. B , densitometric evaluation of PNLIP band intensities in the conditioned media and cell lysates; and assessment of PNLIP enzyme activities in the conditioned media. Samples for all the experiments were collected 48 h after transfection. Mean ± SD of 3 to 5 independent biological replicates are shown. Note that some data points exhibit overlap. ∗ p ≤ 0.05; ∗∗∗ p ≤ 0.001.

Article Snippet: Human Embryonic Kidney (HEK) 293T cells (Merck) were cultured and grown overnight in 2 ml of high-glucose DMEM cell culture media containing 10% FBS, 4 mM glutamine, 50 U/ml penicillin, and 50 μg/ml streptomycin in a 6-well tissue culture plate (1.2 million/well).

Techniques: Transfection, SDS Page, Staining, Western Blot