Journal: Archives of Toxicology

Article Title: The safety of nanostructured synthetic amorphous silica (SAS) as a food additive (E 551)

doi: 10.1007/s00204-016-1850-4

Figure Lengend Snippet: Genotoxicity of silica in vitro (including data of non-food-grade and colloidal SAS)

Article Snippet: HT-29 human colon carcinoma cell line , Pyrogenic SAS (AEROSIL ® 200, AEROSIL ® Ox50) , 12, 40 nm, 200, 50 m 2 /g , Evonik Industries , Cytotoxicity (±FCS, 1 and 10 %, 0.03–156.3 μg/cm 2 ); comet assay with and without Fpg , Negative, no oxidative DNA damage , Gehrke et al. ( ) .

Techniques: In Vitro, Mutagenesis, Spot Test, Derivative Assay, Single Cell Gel Electrophoresis, Incubation, Positive Control, Alkaline Single Cell Gel Electrophoresis

Journal: BMJ Open Respiratory Research

Article Title: Differential response to bacteria, and TOLLIP expression, in the human respiratory tract

doi: 10.1136/bmjresp-2014-000046

Figure Lengend Snippet: TOLLIP expression in nasal and alveolar epithelium. (A) T84 cells were plated at two different cell densities: 5×10 5 per well (lanes 1, 2); 2×10 6 , (lanes 3, 4). Lane 5 represents a negative control without the reverse transcriptase. GAPDH was used as a housekeeping gene. (B) TOLLIP expression was quantified in primary nasal and alveolar epithelium. *p<0.05 by Mann-Whitney U test. (C and D) Cell lines were infected with Staphylococcus aureus strain Newman. RNA extraction was performed followed by RT-PCR. Panel C shows RPMI 2650 cells—and panel D A549 cells—infected with S. aureus . Lanes: (1) positive control for TOLLIP from cell line T84; (2 and 3) unstimulated; (4 and 5) cells with S. aureus at 1.1×10 5 cfu/mL; (6 and 7) cells with S. aureus at 1.6×10 5 cfu/mL. GAPDH was used as a housekeeping gene. Band size for TOLLIP 347 bp and for GAPDH 727 bp (TOLLIP, Toll-interacting protein; RT-PCR, reverse transcriptase PCR).

Article Snippet: The human colonic carcinoma cell line T84 and the human nasal carcinoma cell line RPMI 2650 were from LGC Promochem (Manassas, Virginia, USA; ATCC numbers CCL-248 and CCL-30 respectively).

Techniques: Expressing, Negative Control, Reverse Transcription, MANN-WHITNEY, Infection, RNA Extraction, Reverse Transcription Polymerase Chain Reaction, Positive Control

Journal: Biochemistry and Biophysics Reports

Article Title: Identification and multi-omics analysis of essential coding and long non-coding genes in colorectal cancer

doi: 10.1016/j.bbrep.2025.101938

Figure Lengend Snippet: Identification of CRC ESPs using CRISPR loss-of-function screen and scRNA-seq datasets. a. The pie chart displays the CRC cell line types in the CRISPR loss-of-function screen samples. b. Overlapping ratios between previously identified pan-cancer ESP sets and our results with different ranking proportion cutoffs. c. Average expression levels of CRC ESPs in tumor and normal epithelial cells. d. Functional enrichment analysis of 74 overexpressed CRC ESPs. e. Comparison of CERES scores among different ESP sets. f. Overlap between CRC ESPs or randomly selected genes and three pan-cancer ESP sets. g. The venn diagram illustrates the intersection of different ESP sets. h. The effect of CTNNB1 and NDUFB9 knockout by CRISPR/Cas9 on the survival of HCT116 cell lines.

Article Snippet: HCT116 (human colon carcinoma cell line, Ubigene, YC-C004) were cultured in RPMI-1640 (Thermo Fisher Scientific) with 10 % fetal bovine serum (FBS; VISTECH) and 1 % penicillin-streptomycin (Thermo Fisher Scientific).

Techniques: CRISPR, Expressing, Functional Assay, Comparison, Knock-Out

Journal: Biochemistry and Biophysics Reports

Article Title: Identification and multi-omics analysis of essential coding and long non-coding genes in colorectal cancer

doi: 10.1016/j.bbrep.2025.101938

Figure Lengend Snippet: Prediction of CRC ESLs using co-expression networks. a. The workflow of predicting CRC ESLs. The Venn diagram displays the intersection of predicted CRC ESLs from the two methods. b. The distributions of adjusted p -value for different ESP sets by HT method based on unWCN-TCGA and unWCN-TEC. c. The distributions of PPR rank scores for different ESP sets based on WCN-TCGA and WCN-TEC. d. The expression levels of CRC ESLs in CRC tumor and normal epithelial cells. Genes marked in red indicate significantly overexpression in tumor cells. e. The effect of ESLs knockout by CRISPR/Cas9 on survival of HCT116 cell line. f. The functional annotation of ESLs in CRC. Red block indicates publication-reported functions of lncRNAs in pan-cancer, blue block represents publication-reported properties of lncRNAs, and white block signifies the absence of publication reports.

Article Snippet: HCT116 (human colon carcinoma cell line, Ubigene, YC-C004) were cultured in RPMI-1640 (Thermo Fisher Scientific) with 10 % fetal bovine serum (FBS; VISTECH) and 1 % penicillin-streptomycin (Thermo Fisher Scientific).

Techniques: Expressing, Over Expression, Knock-Out, CRISPR, Functional Assay, Blocking Assay

Journal: Biochemistry and Biophysics Reports

Article Title: Identification and multi-omics analysis of essential coding and long non-coding genes in colorectal cancer

doi: 10.1016/j.bbrep.2025.101938

Figure Lengend Snippet: Expression, DNA mutation, and DNA methylation patterns of CRC essential genes. a. The violin plot shows the gene sets enrichment scores of CRC ESPs, ESLs, other pan-cancer ESP sets, and Hart's non-ESPs in different cell lineages between tumor and normal samples. The yellow line represents the mean score of CRC ESPs in tumor epithelial cells. b. Four CRC ESPs were specifically expressed in tumor epithelial cells compared with other cell lineages. c. The effect of four CRC ESPs knockout by CRISPR/Cas9 on survival of HCT116 cell lines. d-e. The top mutated CRC ESPs (d) and ESLs (e) based on WGS datasets of PCAWG. f. The correlation between PVT1 expression and DNA methylation levels of three probes.

Article Snippet: HCT116 (human colon carcinoma cell line, Ubigene, YC-C004) were cultured in RPMI-1640 (Thermo Fisher Scientific) with 10 % fetal bovine serum (FBS; VISTECH) and 1 % penicillin-streptomycin (Thermo Fisher Scientific).

Techniques: Expressing, Mutagenesis, DNA Methylation Assay, Knock-Out, CRISPR