Journal: Nucleic Acids Research

Article Title: Lineage-determining transcription factor-driven promoters regulate cell type-specific macrophage gene expression

doi: 10.1093/nar/gkae088

Figure Lengend Snippet: Characterizing the major cistromes of BMDMs. (A-D) Cistromes of related TFs were filtered and united to aggregate cistromes; those of the ETS family with IRF8 ( A ) and the bZIP ( B ), bHLH ( C ) and MEF2 families ( D ). Heat maps represent the aggregate cistromes clustered and sorted based on TF densities (left). The scale of densities ranges from 0 to 3. The extent of DNA methylation (Bisulfite-seq, scale: 0–0.1) and chromatin openness (ATAC-seq, scale: 0–20) in 1-kb windows and nascent transcription (GRO-seq, scale: 0–20) in 2-kb windows for each region (middle) and the genomic distribution of the regions relative to the closest TSS (right) are depicted. For the latter, the average distance of 100 consecutive regions on the heat maps was calculated. ( E ) Violin plot represents the genomic distribution of the indicated cistromes relative to the closest TSS.

Article Snippet: Histograms representing the distribution of reads, nucleotides, CG dinucleotides and other sequences, or TSSs at different genomic loci, histograms representing the distribution of peaks relative to the closest TSS, violin plots representing the distance distribution of cistromes or putative elements relative to the closest TSS, violin plots representing ATAC-seq and GRO-seq densities, as well as scatter plots, box plots, bar charts, and a pie chart were visualized by GraphPad Prism v8.0.1.

Techniques: DNA Methylation Assay, Bisulfite Sequencing

Journal: Nucleic Acids Research

Article Title: Lineage-determining transcription factor-driven promoters regulate cell type-specific macrophage gene expression

doi: 10.1093/nar/gkae088

Figure Lengend Snippet: Identification of macrophage-specific promoter classes. ( A ) Pie chart represents the ratio of putative promoters with the indicated composition. ( B ) Box plot represents the levels of nascent transcripts (GRO-seq) originating from the different classes of promoters indicated. Whiskers are plotted according to the Tukey method. ( C ) The distribution of TSSs (CAGE), the identified motifs, and CG sites and the extent of DNA methylation (Bisulfite-seq), chromatin openness (ATAC-seq), H3K27ac and H3K4me3 modifications (MC, MNase-ChIP-seq), and nascent transcription (GRO-seq) are depicted in 1-kb windows around the top TSSs at the indicated promoter classes (TSS selection is detailed in the Methods section). (D–I) Histograms show the distribution of CG sites ( D ), the extent of DNA methylation ( E ), the H3K27ac ( F ) and H3K4me3 modifications ( G ) and nascent transcription (H, I) around the top TSSs at the indicated promoter classes. ( J ) Line plots represent per-position nucleotide frequencies around the top TSSs at the promoters with distal elements only (left) or proximal elements only (right).

Article Snippet: Histograms representing the distribution of reads, nucleotides, CG dinucleotides and other sequences, or TSSs at different genomic loci, histograms representing the distribution of peaks relative to the closest TSS, violin plots representing the distance distribution of cistromes or putative elements relative to the closest TSS, violin plots representing ATAC-seq and GRO-seq densities, as well as scatter plots, box plots, bar charts, and a pie chart were visualized by GraphPad Prism v8.0.1.

Techniques: DNA Methylation Assay, Bisulfite Sequencing, ChIP-sequencing, Selection

Journal: Nucleic Acids Research

Article Title: Lineage-determining transcription factor-driven promoters regulate cell type-specific macrophage gene expression

doi: 10.1093/nar/gkae088

Figure Lengend Snippet: Characteristics of LDTF-driven promoters. ( A ) Scatter plot represents correlations between the nascent (GRO-seq) and mature mRNA levels (RNA-seq) associated with LDTF-driven promoters. ( B ) GO terms (Biological processes) specific to LDTF-driven promoters are shown. ( C ) Putative models (top) and examples (bottom) for LDTF-driven (left) and CGI promoters (right) are shown. Model: Arrows represent TSSs and transcription initiation frequencies. Greyscale, white, red, and light gold boxes represent respectively methylatable, non-methylated, and prototypically TSS-distal or proximal non-methylatable elements. Black, greyscale and white circles represent respectively methylated, potentially methylated, and non-methylated cytosines. LDTF: lineage-determining TF, CBTF: CGI-binding TF. Genome browser views show the chromatin openness (dark olive), nascent transcription (light and dark green, strand specifically), mRNA level (dark grey), the density of CG (light blue) and methyl-CG dinucleotides (blue), and the distribution of elements (black and red boxes) of representative genes (middle) and promoters (bottom).

Article Snippet: Histograms representing the distribution of reads, nucleotides, CG dinucleotides and other sequences, or TSSs at different genomic loci, histograms representing the distribution of peaks relative to the closest TSS, violin plots representing the distance distribution of cistromes or putative elements relative to the closest TSS, violin plots representing ATAC-seq and GRO-seq densities, as well as scatter plots, box plots, bar charts, and a pie chart were visualized by GraphPad Prism v8.0.1.

Techniques: RNA Sequencing, Methylation, Binding Assay

Journal: Molecular cell

Article Title: Transcriptional responses to IFN-γ require Mediator kinase-dependent pause release and mechanistically distinct functions of CDK8 and CDK19

doi: 10.1016/j.molcel.2019.07.034

Figure Lengend Snippet: Key Resource Table

Article Snippet: Mix2 RNA-Seq data analysis software , Lexogen , .

Techniques: Virus, Recombinant, Transfection, Protease Inhibitor, Reverse Transcription, Isolation, Lysis, Gel Extraction, Plasmid Preparation, Western Blot, Expressing, Cloning, Software

Journal: STAR Protocols

Article Title: Co-staining human PBMCs with fluorescent antibodies and antibody-oligonucleotide conjugates for cell sorting prior to single-cell CITE-Seq

doi: 10.1016/j.xpro.2021.100893

Figure Lengend Snippet:

Article Snippet: SeqGeq™ v1.6.0 software (analysis and visualization of single-cell CITE-Seq data) , BD Biosciences , https://www.flowjo.com/solutions/seqgeq.

Techniques: Recombinant, Staining, Cell Culture, Blocking Assay, Amplification, Software, Sequencing, Flow Cytometry, Transferring