Journal: Immunity

Article Title: m 6 A Modification Prevents Formation of Endogenous Double-Stranded RNAs and Deleterious Innate Immune Responses during Hematopoietic Development

doi: 10.1016/j.immuni.2020.05.003

Figure Lengend Snippet: KEY RESOURCES TABLE

Article Snippet: Cat# 10010200; RRID: AB_2651015 Cy3 Streptavidin VECTOR LABORATORIES Cat# SA-1300 Cy5 Streptavidin VECTOR LABORATORIES Cat# SA-1500 Chemicals, Peptides, and Recombinant Proteins MethoCult™ GF M3434 STEMCELL Technologies Cat# 03434 Phusion High-Fidelity PCR Master Mix with HF Buffer New England Biolabs Cat# M0531L RBC Lysis Buffer, 10X Santa Cruze Biotechnology Cat# sc-296258 Lipofectamine™ 2000 Transfection Reagent ThermoFisher SCIENTIFIC Cat# 11668019 Lipofectamine™ RNAiMAX Transfection Reagent ThermoFisher SCIENTIFIC Cat# 13778100 Mouse Thrombopoietin (mTPO) Gemini Bio-product Cat# 300-351P Mouse Stem Cell Factor (mSCF) Gemini Bio-product Cat# 300-348P Mouse Flt-3 Ligand (mFlt3L) Gemini Bio-product Cat# 300-306P Mouse Interleukin-3 (mIL3) Gemini Bio-product Cat# 300-324P Benchmark Fetal Bovine Serum (FBS) Gemini Bio-product Cat# 100-106 DMEM, high glucose ThermoFisher SCIENTIFIC Cat# 11965092 Protein A–micrococcal nuclease (pA-MN) fusion protein Henikoff lab Skene and Henikoff, 2018 Spermidine trihydrochloride Sigma-Aldrich Cat# S2501 Con A-coated BioMag®Plus microparticles Polysciences, Inc Cat# 86057-3 iQ™ SYBR® Green Supermix BIO-RAD Cat# 1708880 iScript cDNA Synthesis Kit BIO-RAD Cat# 1708890 cOmplete™, Mini, EDTA-free Protease Inhibitor Cocktail Sigma-Aldrich Cat# 11836170001 SUPERase• In™ RNase Inhibitor ThermoFisher SCIENTIFIC Cat# AM2696 SPRIselect beads Beckman Coulter Cat# {"type":"entrez-nucleotide","attrs":{"text":"B23317","term_id":"2508948","term_text":"B23317"}} B23317 RNaseA, Dnase and protease-free ThermoFisher SCIENTIFIC Cat# EN0531 Maxima H Minus Reverse Transcriptase ThermoFisher SCIENTIFIC Cat# EP0752 Exonuclease I New England Biolabs Cat# M0293S Ampure XP beads Beckman Coulter Cat# A63880 Fluorinert™ FC-40 Sigma-Aldrich Cat# F9755 Critical Commercial Assays EpiQuik m 6 A RNA Methylation Quantification Kit (Colorimetric) Epigentek Cat# P-9005-96 FITC BrdU Flow Kits BD Pharmingen™ Cat# 559619 CellTrace CFSE Cell Proliferation Kit, for flow Thermo Fisher Cat# {"type":"entrez-nucleotide","attrs":{"text":"C34554","term_id":"2370695","term_text":"C34554"}} C34554 FITC Annexin V Apoptosis Detection Kit I BD Pharmingen™ Cat# 556547 RNeasy Mini Kit QIAGEN Cat# 74106 RNeasy Plus Micro Kit QIAGEN Cat# 74034 Magnetic mRNA Isolation Kit New England Biolabs Cat# S1550S MinElute PCR Purification Kit QIAGEN Cat# 28004 NEBNext Multiplex Oligos for Illumina New England Biolabs Cat# E7500S NEBNext Ultra II DNA Library Prep Kit New England Biolabs Cat# E7645S Qubit dsDNA HS Assay Kit Life Technologies Cat# {"type":"entrez-protein","attrs":{"text":"Q32851","term_id":"75280859","term_text":"Q32851"}} Q32851 Vector M.O.M.

Techniques: Purification, Blocking Assay, Plasmid Preparation, Recombinant, Lysis, Transfection, SYBR Green Assay, Protease Inhibitor, Methylation, Isolation, Multiplex Assay, Immunodetection, Software, Sequencing

Journal: Immunity

Article Title: m 6 A Modification Prevents Formation of Endogenous Double-Stranded RNAs and Deleterious Innate Immune Responses during Hematopoietic Development

doi: 10.1016/j.immuni.2020.05.003

Figure Lengend Snippet: KEY RESOURCES TABLE

Article Snippet: Cat# 10010200; RRID: AB_2651015 Cy3 Streptavidin VECTOR LABORATORIES Cat# SA-1300 Cy5 Streptavidin VECTOR LABORATORIES Cat# SA-1500 Chemicals, Peptides, and Recombinant Proteins MethoCult™ GF M3434 STEMCELL Technologies Cat# 03434 Phusion High-Fidelity PCR Master Mix with HF Buffer New England Biolabs Cat# M0531L RBC Lysis Buffer, 10X Santa Cruze Biotechnology Cat# sc-296258 Lipofectamine™ 2000 Transfection Reagent ThermoFisher SCIENTIFIC Cat# 11668019 Lipofectamine™ RNAiMAX Transfection Reagent ThermoFisher SCIENTIFIC Cat# 13778100 Mouse Thrombopoietin (mTPO) Gemini Bio-product Cat# 300-351P Mouse Stem Cell Factor (mSCF) Gemini Bio-product Cat# 300-348P Mouse Flt-3 Ligand (mFlt3L) Gemini Bio-product Cat# 300-306P Mouse Interleukin-3 (mIL3) Gemini Bio-product Cat# 300-324P Benchmark Fetal Bovine Serum (FBS) Gemini Bio-product Cat# 100-106 DMEM, high glucose ThermoFisher SCIENTIFIC Cat# 11965092 Protein A–micrococcal nuclease (pA-MN) fusion protein Henikoff lab Skene and Henikoff, 2018 Spermidine trihydrochloride Sigma-Aldrich Cat# S2501 Con A-coated BioMag®Plus microparticles Polysciences, Inc Cat# 86057-3 iQ™ SYBR® Green Supermix BIO-RAD Cat# 1708880 iScript cDNA Synthesis Kit BIO-RAD Cat# 1708890 cOmplete™, Mini, EDTA-free Protease Inhibitor Cocktail Sigma-Aldrich Cat# 11836170001 SUPERase• In™ RNase Inhibitor ThermoFisher SCIENTIFIC Cat# AM2696 SPRIselect beads Beckman Coulter Cat# {"type":"entrez-nucleotide","attrs":{"text":"B23317","term_id":"2508948","term_text":"B23317"}} B23317 RNaseA, Dnase and protease-free ThermoFisher SCIENTIFIC Cat# EN0531 Maxima H Minus Reverse Transcriptase ThermoFisher SCIENTIFIC Cat# EP0752 Exonuclease I New England Biolabs Cat# M0293S Ampure XP beads Beckman Coulter Cat# A63880 Fluorinert™ FC-40 Sigma-Aldrich Cat# F9755 Critical Commercial Assays EpiQuik m 6 A RNA Methylation Quantification Kit (Colorimetric) Epigentek Cat# P-9005-96 FITC BrdU Flow Kits BD Pharmingen™ Cat# 559619 CellTrace CFSE Cell Proliferation Kit, for flow Thermo Fisher Cat# {"type":"entrez-nucleotide","attrs":{"text":"C34554","term_id":"2370695","term_text":"C34554"}} C34554 FITC Annexin V Apoptosis Detection Kit I BD Pharmingen™ Cat# 556547 RNeasy Mini Kit QIAGEN Cat# 74106 RNeasy Plus Micro Kit QIAGEN Cat# 74034 Magnetic mRNA Isolation Kit New England Biolabs Cat# S1550S MinElute PCR Purification Kit QIAGEN Cat# 28004 NEBNext Multiplex Oligos for Illumina New England Biolabs Cat# E7500S NEBNext Ultra II DNA Library Prep Kit New England Biolabs Cat# E7645S Qubit dsDNA HS Assay Kit Life Technologies Cat# {"type":"entrez-protein","attrs":{"text":"Q32851","term_id":"75280859","term_text":"Q32851"}} Q32851 Vector M.O.M.

Techniques: Purification, Blocking Assay, Plasmid Preparation, Recombinant, Lysis, Transfection, SYBR Green Assay, Protease Inhibitor, Methylation, Isolation, Multiplex Assay, Immunodetection, Software, Sequencing

Journal: bioRxiv

Article Title: Potential of HLA-E-targeting diabodies to induce lysis of HIV-1-infected cells by CD8 + T cells

doi: 10.64898/2026.04.28.721204

Figure Lengend Snippet: Specificity of RLP-13 in dual-color co-cultures. (A) Setup of dual-color co-cultures: K562 cells transfected with covalently linked peptide:HLA-E expression constructs, presenting either cognate (Mtb44) or non-cognate (SP-2A) peptide, are stained with CellTrace Violet (CTV) or CFSE, respectively, and cultured for 18 hours with pre-expanded CD8 + T cells and different concentrations of RLP-13 at a ratio of 4:1:3 (Effector : Cognate target : Non-cognate target). Cells are then stained with lineage and activation markers and viability dye for analysis by flow cytometry. (B) Representative flow plot of viable single cell populations from co-culture wells without (left) or with (right) RLP-13. Indicated cognate and non-cognate gated population frequencies were used to calculate the relative viability of target cell populations. (C) Target cell viability of indicated cognate and non-cognate populations from co-cultures with various concentrations of either RLP-13 (red and pink lines) or irrelevant control scDb H2-mu (black and green lines). Viability was calculated by normalizing the frequency of the indicated target cell populations to that observed in co-culture wells without any scDb added. Assay was repeated five independent times across two HIV-negative donors. Shown measurements are averaged over eight technical replicates from one representative experiment. (D) Concentrations of the indicated effector molecules in the supernatants of co-cultures shown in (C) measured using the LegendPlex CD8/NK cell cytokine panel kit.

Article Snippet: For our dual-color co-culture , pulsed cells were incubated for 15 minutes in PBS with CellTrace Violet or CFSE (FisherScientific, Cat. # C34557) or CFSE (FisherScientific, Cat. # C34554) at a 1:20,000 dilution.

Techniques: Transfection, Expressing, Construct, Staining, Cell Culture, Activation Assay, Flow Cytometry, Single Cell, Co-Culture Assay, Control

Journal: eLife

Article Title: Disturbed retinoid metabolism upon loss of rlbp1a impairs cone function and leads to subretinal lipid deposits and photoreceptor degeneration in the zebrafish retina

doi: 10.7554/eLife.71473

Figure Lengend Snippet:

Article Snippet: After washing with 1× PBS, samples were stained with CellTrace BODIPY TR methyl ester (1:200 in PDT [1 % dimethyl sulfoxide, 0.1 % Triton X-100 in PBS], cat# C34556, Thermo Fisher Scientific, Waltham, MA) for 20 min at RT and washed again with 1× PBS.

Techniques: Mutagenesis, CRISPR, Sequencing, Recombinant, SYBR Green Assay, Electron Microscopy, Software