Journal: Cell reports

Article Title: Single-Cell RNA-Sequencing-Based CRISPRi Screening Resolves Molecular Drivers of Early Human Endoderm Development

doi: 10.1016/j.celrep.2019.03.076

Figure Lengend Snippet: KEY RESOURCES TABLE

Article Snippet: Primary antibodies used in this study include: SOX17 antibody (1:300; R&D Systems, AF1924), OCT3/4 antibody (1:100; Santa Cruz Biotechnology, sc5279), FOXA2 antibody (1:300; Millipore EMD, 07–633), CDX2 antibody (1:300; BioGenex, MU392A-UC), HNF4A antibody (1:500; Abcam, ab41898), HHEX antibody (1:500; R&D Systems, MAB83771), TBX3 antibody (1:300; Santa Cruz Biotechnology, sc17871), PROX1 antibody (1:300; R&D Systems, AF2727), EPCAM antibody (1:1000; Biolegend, 324202).

Techniques: Recombinant, Staining, Transfection, DNA Library Preparation, Methylation, Software, Fluorescence, Microscopy

Journal: International Journal of Molecular Sciences

Article Title: Unraveling the Influence of HHEX Risk Polymorphism rs7923837 on Multiple Sclerosis Pathogenesis

doi: 10.3390/ijms23147956

Figure Lengend Snippet: mRNA and protein expression of HHEX. ( A ) mRNA expression in controls, multiple sclerosis (MS) patients, and MS patients stratified by treatment. Controls: n = 117; MS patients: n = 154; MS patients treated with IFN-β: n = 94; MS patients treated with glatiramer acetate: n = 57. ( B ) HHEX mRNA expression in controls and MS patients stratified by rs7923837 genotype. Heterozygotes were grouped with major homozygotes due to similar expression levels. Control GG + GA: n = 101; minor allele homozygous controls AA: n = 16; MS GG + GA: n = 133; MS AA: n = 18; MS GG + GA treated with IFN-β: n = 85; MS AA treated with IFN-β: n = 9; MS GG + GA treated with glatiramer acetate: n = 48; MS AA treated with glatiramer acetate: n = 9. ( C ) Expression of HHEX protein analyzed by Western blot, stratified by rs7923837 genotype. Control GG + GA: n = 24; Control AA: n = 9; MS GG + GA: n = 36; MS AA: n = 13. Mean and standard deviation are presented in all panels.

Article Snippet: Cells were stained with rabbit anti-human HHEX (HPA055460, Atlas Antibodies, Bromma, Sweden) as primary antibody, and a combination of biotinylated anti-rabbit antibody (BA-1000, Vector Laboratories, Newark, CA, USA) and streptavidin-Alexa Fluor 555 (S32355, Invitrogen, Waltham, MA, USA) supplemented with Draq5 (ab108410, Abcam, Cambridge, United Kingdom).

Techniques: Expressing, Control, Western Blot, Standard Deviation

Journal: International Journal of Molecular Sciences

Article Title: Unraveling the Influence of HHEX Risk Polymorphism rs7923837 on Multiple Sclerosis Pathogenesis

doi: 10.3390/ijms23147956

Figure Lengend Snippet: Subcellular localization of HHEX by confocal microscopy and epistatic interaction HHEX - BCL6 . ( A ) Immunofluorescence of HHEX by confocal microscopy shows a higher localization of the transcription factor in the nucleus in rs7923837*AA multiple sclerosis (MS) patients. One confocal plane of each condition is shown. ( B ) Cytoplasmic/nuclear HHEX ratio measured by immunofluorescence and stratified by rs7923837 genotypes. Control carriers of the major allele GG + GA: n = 320 cells from 8 subjects; minor allele homozygous controls AA: n = 128 cells from 4 subjects; MS GG + GA: n = 599 cells from 17 subjects; and MS AA: n = 256 cells from 8 subjects. Red lines represent the median of the distribution (Control GG + GA median = 0.48; Control AA median = 0.56; MS GG + GA median = 0.52; MS AA median = 0.39). ( C ) HHEX mRNA expression stratified by the MS-risk polymorphism located near BCL6 , rs2590438. Control carriers of the major allele TT + GT: n = 38; minor allele homozygous controls GG: n = 9; MS TT + GT: n = 40; and MS GG: n = 6. Mean and standard deviation are presented.

Article Snippet: Cells were stained with rabbit anti-human HHEX (HPA055460, Atlas Antibodies, Bromma, Sweden) as primary antibody, and a combination of biotinylated anti-rabbit antibody (BA-1000, Vector Laboratories, Newark, CA, USA) and streptavidin-Alexa Fluor 555 (S32355, Invitrogen, Waltham, MA, USA) supplemented with Draq5 (ab108410, Abcam, Cambridge, United Kingdom).

Techniques: Confocal Microscopy, Immunofluorescence, Control, Expressing, Standard Deviation

Journal: International Journal of Molecular Sciences

Article Title: Unraveling the Influence of HHEX Risk Polymorphism rs7923837 on Multiple Sclerosis Pathogenesis

doi: 10.3390/ijms23147956

Figure Lengend Snippet: Glycolytic profile and mitochondrial mass of PBMCs from multiple sclerosis (MS) patients and controls stratified by the genotypes of HHEX rs7923837. ( A ) Energy phenotype of the studied groups. Minimum and maximum values of extracellular acidification rate (ECAR) and oxygen consumption rate (OCR) were confronted to obtain an estimation of the metabolic range of the cells. ( B – D ) Glycolytic analysis comparing carriers of the major allele in HHEX rs7923837 and minor-allele homozygotes from both MS patients and controls. Control GG + GA: n = 11; Control AA: n = 7; MS GG + GA: n = 18; MS AA: n = 7. ( E – H ) Increase in mitochondrial mass measured by flow cytometry with Mitotracker Green TM after activation with PHA. The ratio of the median fluorescence intensity in the presence/absence of PHA was calculated for PBMCs ( E ) and the indicated lymphocyte subpopulations ( F – H ). Control GG + GA: n = 9; Control AA: n = 5; MS GG + GA: n = 17; MS AA: n = 8. Mean and standard deviation are presented in panels ( B – H ).

Article Snippet: Cells were stained with rabbit anti-human HHEX (HPA055460, Atlas Antibodies, Bromma, Sweden) as primary antibody, and a combination of biotinylated anti-rabbit antibody (BA-1000, Vector Laboratories, Newark, CA, USA) and streptavidin-Alexa Fluor 555 (S32355, Invitrogen, Waltham, MA, USA) supplemented with Draq5 (ab108410, Abcam, Cambridge, United Kingdom).

Techniques: Control, Flow Cytometry, Activation Assay, Fluorescence, Standard Deviation