Journal: eLife

Article Title: KRAB-zinc finger protein gene expansion in response to active retrotransposons in the murine lineage

doi: 10.7554/eLife.56337

Figure Lengend Snippet: ( A ) Differential analysis of summative (all individual insertions combined) H3K9me3 enrichment at TE groups in Chr10-cl, Chr13.1-cl and Chr13.2-cl KO ES cells. TE groups targeted by one or several KRAB-ZFPs encoded within the deleted clusters are highlighted in orange (differential enrichment over the entire TE sequences) and red (differential enrichment at TE regions that overlap with KRAB-ZFP ChIP-seq peaks). ( B ) Top: Schematic view of the Cd59a / Cd59b locus with a 5’ truncated ETn insertion. ChIP-seq (Input subtracted from ChIP) data for overexpressed epitope-tagged Gm13051 (a Chr4-cl KRAB-ZFP) in F9 EC cells, and re-mapped KAP1 (GEO accession: GSM1406445) and H3K9me3 (GEO accession: GSM1327148) in WT ES cells are shown together with RNA-seq data from Chr4-cl WT and KO ES cells (mapped using Bowtie (-a -m 1 -- strata -v 2) to exclude reads that cannot be uniquely mapped). Bottom: Transcriptional activity of a 5 kb fragment with or without fragments of the ETn insertion was tested by luciferase reporter assay in Chr4-cl WT and KO ES cells.

Article Snippet: Cell line ( Mus musculus ) , F9 Embryonic carcinoma cells , ATCC , ATCC CRL-1720 , .

Techniques: ChIP-sequencing, RNA Sequencing, Activity Assay, Luciferase, Reporter Assay

Journal: eLife

Article Title: KRAB-zinc finger protein gene expansion in response to active retrotransposons in the murine lineage

doi: 10.7554/eLife.56337

Figure Lengend Snippet: ( A ) Differential gene expression in Chr2-cl and Chr4-cl KO ES cells. Significantly up- and downregulated genes ( adjusted p-value <0.05) are highlighted in red and green, respectively, KRAB-ZFP genes within the deleted clusters are shown in blue. ( B ) Correlation of TEs and gene deregulation. Plots show enrichment of TE groups within 100 kb of up- and downregulated genes relative to all genes. Significantly overrepresented LTR and LINE groups ( adjusted p-value <0.1) are highlighted in blue and red, respectively. ( C ) Schematic view of the downstream region of Chst1 where a 5’ truncated ETn insertion is located. ChIP-seq (Input subtracted from ChIP) data for overexpressed epitope-tagged Gm13051 (a Chr4-cl KRAB-ZFP) in F9 EC cells, and re-mapped KAP1 (GEO accession: GSM1406445) and H3K9me3 (GEO accession: GSM1327148) in WT ES cells are shown together with RNA-seq data from Chr4-cl WT and KO ES cells (mapped using Bowtie (-a -m 1 -- strata -v 2) to exclude reads that cannot be uniquely mapped). ( D ) RT-qPCR analysis of Chst1 mRNA expression in Chr4-cl WT and KO ES cells with or without the CRISPR/Cas9 deleted ETn insertion near Chst1 . Values represent mean expression (normalized to Gapdh) from three biological replicates per sample (each performed in three technical replicates) in arbitrary units. Error bars represent standard deviation and asterisks indicate significance (p<0.01, Student’s t-test). n.s.: not significant. ( E ) Mean coverage of ChIP-seq data (Input subtracted from ChIP) in Chr4-cl WT and KO ES cells over 127 full-length ETn insertions. The binding sites of the Chr4-cl KRAB-ZFPs Rex2 and Gm13051 are indicated by dashed lines.

Article Snippet: Cell line ( Mus musculus ) , F9 Embryonic carcinoma cells , ATCC , ATCC CRL-1720 , .

Techniques: Gene Expression, ChIP-sequencing, RNA Sequencing, Quantitative RT-PCR, Expressing, CRISPR, Standard Deviation, Binding Assay

Journal: eLife

Article Title: KRAB-zinc finger protein gene expansion in response to active retrotransposons in the murine lineage

doi: 10.7554/eLife.56337

Figure Lengend Snippet:

Article Snippet: Cell line ( Mus musculus ) , F9 Embryonic carcinoma cells , ATCC , ATCC CRL-1720 , .

Techniques: Recombinant, Expressing, Plasmid Preparation, CRISPR, Construct, Sequencing, Software

Journal: Arteriosclerosis, Thrombosis, and Vascular Biology

Article Title: Sema3F (Semaphorin 3F) Selectively Drives an Extraembryonic Proangiogenic Program

doi: 10.1161/atvbaha.117.308226

Figure Lengend Snippet: Figure 6. Exogenous recombinant Sema3 (class 3 semaphorin)-F impairs Myc degradation and inhibits Thbs1 (thrombospondin 1) expression in in vitro differentiated visceral yolk sac (VYS) epithelial cells (EpCs). A, Mouse F9 teratocarcinoma stem cells differentiated in VYS EpCs express Sema3F receptor Nrp2, as revealed by immunofluorescence staining. B, Stimulation with exogenous rSema3F increases Myc expression and reduces Myc Thr58 phosphorylation in in vitro differentiated VYS EpCs derived from mouse F9 teratocar- cinoma stem cells. C, rSema3F stimulation also decreases the expression of antiangiogenic Thbs1 protein in VYS EpCs derived from mouse F9 teratocarcinoma stem cells. D, The relative fluorescence intensity of Myc, Thr58 phosphorylated Myc, and Thbs1 was mea- sured in VYS EpCs derived from mouse F9 teratocarcinoma stem cells stimulated or not with rSema3F. Data are mean±SEM. n=15 cell aggregates per condition pooled from 3 independent experiments. (***P<0.0001; *P<0.05, Student t test). Scale bars, 25 μm.

Article Snippet: In vitro generation of model of VYS Eps from F9 testicular teratocarcinoma stem cells Mouse testicular epithelium F9 cells (ATCC CRL-1720) were differentiated in VYS Eps as previously described 5, 6 .

Techniques: Recombinant, Expressing, In Vitro, Immunofluorescence, Staining, Phospho-proteomics, Derivative Assay, Fluorescence

Journal: PLoS ONE

Article Title: Expression Profiles of PIWIL2 Short Isoforms Differ in Testicular Germ Cell Tumors of Various Differentiation Subtypes

doi: 10.1371/journal.pone.0112528

Figure Lengend Snippet: Western blot analyses of a panel of cell lines ( A ) and testis with its adjacent tumor ( B ) with an antibody specific to exons 14–16 of PIWIL2. RT-PCR on cDNA from testis, teratoma, TERA1 and NT2/D1 cell lines with primers for exons 2–23 of PIWIL2 mRNA ( C ). Results of siRNA assay: transcription level of PIWIL2 mRNA (exons 8–9) relative to 18S rRNA ( D ) and PIWIL2 protein isoforms in TERA1 and NT2/D1 ( E ).

Article Snippet: Cell lines used in experiments included TERA1 (ATCC HTB-105, testicular embryonal carcinoma ), NT2/D1 (ATCC CRL-1973, pluripotent testicular embryonal carcinoma ), A549 (ATCC CCL-185, lung carcinoma ), T-47D (ATCC HTB-133, mammary gland ductal carcinoma ), HeLa (ATCC CCL-2, cervical adenocarcinoma ), Raji (ATCC CCL-86, Burkitt's lymphoma , ), Jurkat (ATCC TIB-152, acute T-cell leukaemia ), NGP-127 (neuroblastoma, ), IMR-32 (ATCC CCL-127, neuroblastoma ), Daudi (ATCC CCL-213, Burkitt's lymphoma ), A-431 (ATCC CRL-1555, epidermoid carcinoma ), HEK-293 (ATCC CRL-1573, embryonic kidney ), Hep G2 (ATCC HB-8065, hepatocellular carcinoma ) and HL-60 (ATCC CCL-240, acute promyelocytic leukemia ).

Techniques: Western Blot, Reverse Transcription Polymerase Chain Reaction

Journal: PLoS ONE

Article Title: Expression Profiles of PIWIL2 Short Isoforms Differ in Testicular Germ Cell Tumors of Various Differentiation Subtypes

doi: 10.1371/journal.pone.0112528

Figure Lengend Snippet: Results of 5′ and 3′-RACE experiments in TERA1 and NT2/D1 cell lines.

Article Snippet: Cell lines used in experiments included TERA1 (ATCC HTB-105, testicular embryonal carcinoma ), NT2/D1 (ATCC CRL-1973, pluripotent testicular embryonal carcinoma ), A549 (ATCC CCL-185, lung carcinoma ), T-47D (ATCC HTB-133, mammary gland ductal carcinoma ), HeLa (ATCC CCL-2, cervical adenocarcinoma ), Raji (ATCC CCL-86, Burkitt's lymphoma , ), Jurkat (ATCC TIB-152, acute T-cell leukaemia ), NGP-127 (neuroblastoma, ), IMR-32 (ATCC CCL-127, neuroblastoma ), Daudi (ATCC CCL-213, Burkitt's lymphoma ), A-431 (ATCC CRL-1555, epidermoid carcinoma ), HEK-293 (ATCC CRL-1573, embryonic kidney ), Hep G2 (ATCC HB-8065, hepatocellular carcinoma ) and HL-60 (ATCC CCL-240, acute promyelocytic leukemia ).

Techniques:

Journal: PLoS ONE

Article Title: Expression Profiles of PIWIL2 Short Isoforms Differ in Testicular Germ Cell Tumors of Various Differentiation Subtypes

doi: 10.1371/journal.pone.0112528

Figure Lengend Snippet: Promoter activity measured as a ratio of firefly ( Photinus pyralis ) luciferase to Renilla reniformis luciferase luminescence in TERA1 and NT2/D1 cell lines for genomic regions upstream of each putative transcription start sites mapped in 5′-RACE experiments. Basic vector (negative control) is included.

Article Snippet: Cell lines used in experiments included TERA1 (ATCC HTB-105, testicular embryonal carcinoma ), NT2/D1 (ATCC CRL-1973, pluripotent testicular embryonal carcinoma ), A549 (ATCC CCL-185, lung carcinoma ), T-47D (ATCC HTB-133, mammary gland ductal carcinoma ), HeLa (ATCC CCL-2, cervical adenocarcinoma ), Raji (ATCC CCL-86, Burkitt's lymphoma , ), Jurkat (ATCC TIB-152, acute T-cell leukaemia ), NGP-127 (neuroblastoma, ), IMR-32 (ATCC CCL-127, neuroblastoma ), Daudi (ATCC CCL-213, Burkitt's lymphoma ), A-431 (ATCC CRL-1555, epidermoid carcinoma ), HEK-293 (ATCC CRL-1573, embryonic kidney ), Hep G2 (ATCC HB-8065, hepatocellular carcinoma ) and HL-60 (ATCC CCL-240, acute promyelocytic leukemia ).

Techniques: Activity Assay, Luciferase, Plasmid Preparation, Negative Control

Journal: PLoS ONE

Article Title: Expression Profiles of PIWIL2 Short Isoforms Differ in Testicular Germ Cell Tumors of Various Differentiation Subtypes

doi: 10.1371/journal.pone.0112528

Figure Lengend Snippet: A, Schematic exon/intron structure of the full-length PIWIL2 protein. Small boxes connected by lines represent exons and introns (including the dashed new alternative exon 21a), while long horizontal rectangles correspond to the protein product derived from each mRNA variant. White, grey and black shades refer to N-terminal sequence, PAZ domain and PIWI domain, respectively. Arrows above exons indicate transcription initiation positions, while bars depict polyadenylation sites found in RACE experiments (figures above specify positions in PIWIL2 cDNA NM_018068.3). B, C, D, Transcriptional and translational boundaries of PL2L80A in NT2/D1 (panel B ), PL2L60A in TERA1 cell line (panel C ) and PL2L60A in testicular tumor samples (panel D ) with numbers of N-terminal and C-terminal amino acids in each short isoform.

Article Snippet: Cell lines used in experiments included TERA1 (ATCC HTB-105, testicular embryonal carcinoma ), NT2/D1 (ATCC CRL-1973, pluripotent testicular embryonal carcinoma ), A549 (ATCC CCL-185, lung carcinoma ), T-47D (ATCC HTB-133, mammary gland ductal carcinoma ), HeLa (ATCC CCL-2, cervical adenocarcinoma ), Raji (ATCC CCL-86, Burkitt's lymphoma , ), Jurkat (ATCC TIB-152, acute T-cell leukaemia ), NGP-127 (neuroblastoma, ), IMR-32 (ATCC CCL-127, neuroblastoma ), Daudi (ATCC CCL-213, Burkitt's lymphoma ), A-431 (ATCC CRL-1555, epidermoid carcinoma ), HEK-293 (ATCC CRL-1573, embryonic kidney ), Hep G2 (ATCC HB-8065, hepatocellular carcinoma ) and HL-60 (ATCC CCL-240, acute promyelocytic leukemia ).

Techniques: Derivative Assay, Variant Assay, Sequencing

Journal: PLoS ONE

Article Title: Expression Profiles of PIWIL2 Short Isoforms Differ in Testicular Germ Cell Tumors of Various Differentiation Subtypes

doi: 10.1371/journal.pone.0112528

Figure Lengend Snippet: Suggested transcriptional and translational boundaries of PL2L60A in TERA1 and PL2L80A in NT2/D1 cell lines.

Article Snippet: Cell lines used in experiments included TERA1 (ATCC HTB-105, testicular embryonal carcinoma ), NT2/D1 (ATCC CRL-1973, pluripotent testicular embryonal carcinoma ), A549 (ATCC CCL-185, lung carcinoma ), T-47D (ATCC HTB-133, mammary gland ductal carcinoma ), HeLa (ATCC CCL-2, cervical adenocarcinoma ), Raji (ATCC CCL-86, Burkitt's lymphoma , ), Jurkat (ATCC TIB-152, acute T-cell leukaemia ), NGP-127 (neuroblastoma, ), IMR-32 (ATCC CCL-127, neuroblastoma ), Daudi (ATCC CCL-213, Burkitt's lymphoma ), A-431 (ATCC CRL-1555, epidermoid carcinoma ), HEK-293 (ATCC CRL-1573, embryonic kidney ), Hep G2 (ATCC HB-8065, hepatocellular carcinoma ) and HL-60 (ATCC CCL-240, acute promyelocytic leukemia ).

Techniques:

Journal: PLoS ONE

Article Title: Expression Profiles of PIWIL2 Short Isoforms Differ in Testicular Germ Cell Tumors of Various Differentiation Subtypes

doi: 10.1371/journal.pone.0112528

Figure Lengend Snippet: A , Western blot analysis of TERA1 and NT2/D1 cell lines with the 14–16ex PIWIL2 antibody. Untreated HEK-293 cells and specially constructed PIWIL2 short isoforms transiently expressed in HEK-293 cells were used as controls : exons 1 to 15 (1–15), exons 7 to 17 (7–17), exons 7 to 21a (7–21a) and exons 11 to 23 (11–23). B , Transcription level relative to 18S rRNA of exons downstream of the putative transcription initiation sites.

Article Snippet: Cell lines used in experiments included TERA1 (ATCC HTB-105, testicular embryonal carcinoma ), NT2/D1 (ATCC CRL-1973, pluripotent testicular embryonal carcinoma ), A549 (ATCC CCL-185, lung carcinoma ), T-47D (ATCC HTB-133, mammary gland ductal carcinoma ), HeLa (ATCC CCL-2, cervical adenocarcinoma ), Raji (ATCC CCL-86, Burkitt's lymphoma , ), Jurkat (ATCC TIB-152, acute T-cell leukaemia ), NGP-127 (neuroblastoma, ), IMR-32 (ATCC CCL-127, neuroblastoma ), Daudi (ATCC CCL-213, Burkitt's lymphoma ), A-431 (ATCC CRL-1555, epidermoid carcinoma ), HEK-293 (ATCC CRL-1573, embryonic kidney ), Hep G2 (ATCC HB-8065, hepatocellular carcinoma ) and HL-60 (ATCC CCL-240, acute promyelocytic leukemia ).

Techniques: Western Blot, Construct

Journal: PLoS ONE

Article Title: Expression Profiles of PIWIL2 Short Isoforms Differ in Testicular Germ Cell Tumors of Various Differentiation Subtypes

doi: 10.1371/journal.pone.0112528

Figure Lengend Snippet: Western blotting with 14–16ex PIWIL2 antibody and transcription levels of PIWIL2 (exons 8–9), NANOG and OCT4 ( POU5F1 ) relative to 18S rRNA in NT2/D1 ( A ) and TERA1 ( B ) cell lines. (RA+) - experiment with retinoic acid treatment, (RA-) - controls with no treatment.

Article Snippet: Cell lines used in experiments included TERA1 (ATCC HTB-105, testicular embryonal carcinoma ), NT2/D1 (ATCC CRL-1973, pluripotent testicular embryonal carcinoma ), A549 (ATCC CCL-185, lung carcinoma ), T-47D (ATCC HTB-133, mammary gland ductal carcinoma ), HeLa (ATCC CCL-2, cervical adenocarcinoma ), Raji (ATCC CCL-86, Burkitt's lymphoma , ), Jurkat (ATCC TIB-152, acute T-cell leukaemia ), NGP-127 (neuroblastoma, ), IMR-32 (ATCC CCL-127, neuroblastoma ), Daudi (ATCC CCL-213, Burkitt's lymphoma ), A-431 (ATCC CRL-1555, epidermoid carcinoma ), HEK-293 (ATCC CRL-1573, embryonic kidney ), Hep G2 (ATCC HB-8065, hepatocellular carcinoma ) and HL-60 (ATCC CCL-240, acute promyelocytic leukemia ).

Techniques: Western Blot

Journal: Biomolecules

Article Title: Exogenous Selenoprotein V Induces Apoptosis in Murine Testicular Teratoma Cells via Mitochondrial Dysfunction and ROS Overproduction

doi: 10.3390/biom15121733

Figure Lengend Snippet: Effects of 24-h pre-incubation of F9 cells with protein solvent buffer or various concentrations of recombinant SELENOV on cell viability. ( A ) Viability cytogram of F9 cells following treatment with 100 μL/mL (equivalent to 50 μg/mL SELENOV application) or 200 μL/mL (equivalent to 100 μg/mL SELENOV application) of solvent buffer. The 10 μg/mL SELENOV group was compared to the untreated control, as the corresponding buffer volume was negligible. ( B ) Viability cytogram of F9 cells after treatment with different concentrations of recombinant SELENOV. ( C ) Effects of solvent buffer or recombinant SELENOV on cell viability and activation of cell death pathways. Data are presented as mean ± SEM. Statistical significance was determined by one-way ANOVA followed by Tukey’s post hoc test. *** p < 0.001 versus the Control group; ### p < 0.001 versus the corresponding Buffer group.

Article Snippet: The study utilized several established cell lines: F9 cells (a murine embryonal carcinoma model derived from testicular teratoma of C57BL/6 mice) and mouse fibroblasts (L-929), all obtained from the American Type Culture Collection (ATCC, Manassas, VA, USA).

Techniques: Incubation, Solvent, Recombinant, Control, Activation Assay