sk hep 1 cultivation  (ATCC)

Journal: bioRxiv

Article Title: CHPT1–LCAT rewires lipolysis towards ferroptosis

doi: 10.64898/2026.03.15.711301

Figure Lengend Snippet: a–c , Tumour weight of HT-1080 ( a , b ) and SK-HEP-1 ( c ) xenografts measured at the experimental endpoint following the indicated treatments. n = 6 ( a ), 8 ( b ) or 7 ( c ). d , f , Tumours from xenograft experiments were excised and sectioned for 4-HNE immunofluorescence staining; representative images are shown for HT-1080 ( d ) and SK-HEP-1 ( f ). Scale bar, 50 µm. e , g , Quantification of 4-HNE-positive areas corresponding to the images in d and f . n = 8 ( e ) or 7 ( g ), with three random fields quantified per sample. Data in a–c , e and g are mean ± s.d. Statistical analysis in a–c , e and g was performed using one-way ANOVA; ns, not significant; *P < 0.05, **P < 0.01, ***P < 0.001.

Article Snippet: HeLa, A549, HepG2, HEK293T, MCF7, HT-1080, SK-HEP-1, NCI-H226, SNU878 and U251 cell lines were obtained from the American Type Culture Collection (ATCC).

Techniques: Immunofluorescence, Staining

Journal: bioRxiv

Article Title: Non-canonical function of the splicing activator U2AF2 in promoting intron retention in the lncRNAs PURPL and MALAT1

doi: 10.64898/2026.02.19.706780

Figure Lengend Snippet: (A) IGV snapshot of eCLIP-seq data showing binding sites and enrichment of U2AF2 and U2AF1 on the PURPL transcripts around intron 2. eCLIP-seq data for PTBP1, PRPF8, and SRSF1 are indicated. The annotated locus by RefSeq is also indicated. eCLIP data-seq was downloaded from encodeproject.org. (B) RT-qPCR after RNA-IPs using a U2AF2 antibody with primer pairs specifically detecting PURPL transcripts as indicated in Figure S1C. U2AF2 binds to transcripts containing intron 2 but not the ones with intron 1, intron 3, or spliced exons 2 and 3. Samples were normalized to IgG-IP. 18S was used as a loading control. (C) Top panel: Gel with RT-PCR products for PURPL upon knockdown of U2AF2 with 2 different siRNAs in SKHEP1 cells. The schematics next to the gel indicate the expected products of the intron-retained and spliced isoforms. Between the two expected PCR products, we observed an extra band corresponding to the inclusion of an alternative exon inside PURPL intron 2 as observed in RefSeq, the inclusion of which is not affected by U2AF2. Quantitation of the gel bands is shown in the graphs on the right. Bottom panel: Schematic of the PCR primer triplet used to detect intron 2 retention (red) or splicing (purple). The length for each PCR product is indicated. (D) RNA-FISH images for PURPL with intron 2 retention and MALAT1 in HCT116 cells without treatment or after 24 hr of 2 mM of Hydorxyurea (HU) to induce PURPL expression. Scale bar is 10μm. (E) RT-qPCR for intron 2-containing PURPL transcript after 48 hr of 1μg/ml doxycycline treatment in comparison to no treatment in SKHEP1 PURPL -CRISPRi populations using 3 different gRNAs. (F) Proliferation assay showing the effect of overexpression of intron 2-containing PURPL transcript in the proliferation of SKHEP1 cells where the endogenous PURPL is knocked down with CRISPRi. The graph depicts the average of 3 populations with different gRNAs. The cells were treated with 1ug/ml doxycycline to induce intron 2-retained PURPL expression and cell proliferation was monitored at 3 and 6 days. Error bars represent standard deviations from 2 (E,) and 3 (C) experiments. **p<0.01, ***p<0.001.

Article Snippet: HAP1, HCT116, HEK293T, HepG2, RPE1, SKHEP1, U2OS, WI38, and MDA-MB-231 cells were purchased from ATCC and maintained in Dulbecco’s Modified Eagle Medium (DMEM) (Gibco) supplemented with 10% (v/v) fetal bovine serum (Gibco) and 1% (v/v) PenStrep (Gibco) in a 5% CO 2 atmosphere at 37°C.

Techniques: Binding Assay, Quantitative RT-PCR, Control, Reverse Transcription Polymerase Chain Reaction, Knockdown, Quantitation Assay, Expressing, Comparison, Proliferation Assay, Over Expression

Journal: bioRxiv

Article Title: Non-canonical function of the splicing activator U2AF2 in promoting intron retention in the lncRNAs PURPL and MALAT1

doi: 10.64898/2026.02.19.706780

Figure Lengend Snippet: (A) U2AF2 was knocked down in SKHEP1 cells and 72 hr later, RNA was extracted and RNA-seq was performed. Left : Number of decreased (blue) and increased (red) IR events at various p-values after U2AF2 knockdown as analyzed with the IR Finder algorithm. The purple arrow indicates the PURPL IR event and green arrows indicate MALAT IR events Right : Pie chart of the numbers of increased and decreased IR events upon U2AF2 knockdown. (B) Floating bar plot showing the IR ratio of PURPL intron 2 and the IR ratio of intron 1 (middle) and intron 2 (right) of MALAT1 . siCTRL and siU2AF2#1 samples as analyzed with the IRFinder algorithm. (C) and (E) RT-PCR for MALAT1 using a primer pair flanking the regulated intron 1 (C) or intron 2 (E) upon knockdown of U2AF2 with 2 different siRNAs in HCT116 and SKHEP1 cells. The schematics next to the gel indicate the expected products of the intron-retained and spliced isoforms. (D) and (F) Bar graph with quantitation of the gel bands from (C) and (E) in SKHEP1 cells. Error bars represent standard deviations from 2 independent experiments. *p<0.05, **p<0.01, ***p<0.001.

Article Snippet: HAP1, HCT116, HEK293T, HepG2, RPE1, SKHEP1, U2OS, WI38, and MDA-MB-231 cells were purchased from ATCC and maintained in Dulbecco’s Modified Eagle Medium (DMEM) (Gibco) supplemented with 10% (v/v) fetal bovine serum (Gibco) and 1% (v/v) PenStrep (Gibco) in a 5% CO 2 atmosphere at 37°C.

Techniques: RNA Sequencing, Knockdown, Reverse Transcription Polymerase Chain Reaction, Quantitation Assay

Journal: bioRxiv

Article Title: Non-canonical function of the splicing activator U2AF2 in promoting intron retention in the lncRNAs PURPL and MALAT1

doi: 10.64898/2026.02.19.706780

Figure Lengend Snippet: (A) RNA-FISH images for MALAT1 and Immunofluorescence images for SON is shown upon transfection of SKHEP1 cells with siCTRL or siU2AF2. MALAT1 is enriched in nuclear speckles in the siCTRL but not upon U2AF2 knockdown. (B) Quantitation of the speckle to nuclear plasma MALAT1 signal ratio in the three replicates in panel (A) . ****p<0.0001.

Article Snippet: HAP1, HCT116, HEK293T, HepG2, RPE1, SKHEP1, U2OS, WI38, and MDA-MB-231 cells were purchased from ATCC and maintained in Dulbecco’s Modified Eagle Medium (DMEM) (Gibco) supplemented with 10% (v/v) fetal bovine serum (Gibco) and 1% (v/v) PenStrep (Gibco) in a 5% CO 2 atmosphere at 37°C.

Techniques: Immunofluorescence, Transfection, Knockdown, Quantitation Assay, Clinical Proteomics