Journal: Epigenetics

Article Title: Battle of epigenetic proportions: comparing Illumina's EPIC methylation microarrays and TruSeq targeted bisulfite sequencing.

doi: 10.1080/15592294.2019.1656159

Figure Lengend Snippet: Figure 1. Coverage of epigenetic and genetic elements for EPIC (black) and TruSeq (red).

Article Snippet: To fill this gap, we conducted a comparison study in which we processed cord blood samples from four newborns in duplicates using both the Illumina HumanMethylationEPIC BeadChip and the Illumina TruSeq Methyl Capture EPIC Kit, and evaluated both platforms in regard to coverage, reproducibility, and identification of differential methylation.

Techniques:

Journal: Epigenetics

Article Title: Battle of epigenetic proportions: comparing Illumina's EPIC methylation microarrays and TruSeq targeted bisulfite sequencing.

doi: 10.1080/15592294.2019.1656159

Figure Lengend Snippet: Figure 2. Concordance of methylation level estimates between EPIC and TruSeq samples stratified by read depth.

Article Snippet: To fill this gap, we conducted a comparison study in which we processed cord blood samples from four newborns in duplicates using both the Illumina HumanMethylationEPIC BeadChip and the Illumina TruSeq Methyl Capture EPIC Kit, and evaluated both platforms in regard to coverage, reproducibility, and identification of differential methylation.

Techniques: Methylation

Journal: bioRxiv

Article Title: Inducible activation of PKA in osteoblasts causes a profound high bone turnover phenotype similar to human diseases

doi: 10.64898/2026.03.11.709826

Figure Lengend Snippet: Two tibiae from each animal, at 7 weeks of age, were divided into subcortical trabecular-rich bone, bone marrow, and cortical bone (osteocyte-rich bone) Total RNA was isolated. RNAseq was performed on the trabecular-rich area. Three mice per group. (A) The Principal Component Analysis (PGA) plot shows the transcriptomic variances of Prkar1a ob+/+ (blue) and Prkar1a ob-/- (red) samples. PC1, accounting for 73% of the variance, shows a clear separation between the two groups which suggests the substantial transcriptomic differences existing in the overall gene expression profiles between them; while PC2, accounting for 13% indicates less variation within the same groups. (B) Heat Maps of Prkar1a ob+/+ and Prkar1a ob-/- show the regulation of the transcriptomesfrom the two groups of mice. Red represents transcript upregulation; blue represents transcript downregulation. Analysis is relative to control (Prkar1a ob+/+ ) samples. Genes were selected if they had a Log2 fold change (FC) > 1 and had a False Discovery Rate (FDR) < 0.05. (C) Volcano Plot of Prkar1a ob-/- to Prkarla ob+/+ shows the regulation of the transcriptome. Genes were selected if they had a Log2 fold change (FC) > 1 and a False Discovery Rate (FDR) < 0.05. Genes in red on the graph are significantly regulated, while blue genes show no significant changes compared to control mice. Blue arrows point to particular genes (Bglap or osteocalcin and Sosf) which are down regulated in Prkar1a ob-/- mice compared to their controls and a red arrow indicates the Ibsp gene upregulation in Prkar1a ob-/- mice. (D) Pathway-specific analysis by Gene Ontology for Biological Processes. (E-N) qRT-PCR was performed and osteoblastic gene expression was measured. (E-l) Trabecular-rich tibial bone; (E) Bone sialoprotein (tbsp), (F) osteocalcin or Bglap, (G) Sosf, and PTH-responsive genes: (H) Tnfsf11 and (I) Mmp13. (J-N) Osteocyte-rich cortical tibial bone: (J) Bone siaioprotein (Ibsp), (K) Osteocalcin or Bglap, (L) Sost, and PTH-responsive genes: (M) Tnfsf11 and (N) Mmp13 Nine to twelve mice per group. Results are means ± SD

Article Snippet: The RNA-seq libraries were constructed using the Illumina TruSeq Stranded Total RNA library prep kit with Ribozero Gold (San Diego, CA).

Techniques: Isolation, RNA sequencing, Gene Expression, Control, Quantitative RT-PCR

Journal: bioRxiv

Article Title: Inducible activation of PKA in osteoblasts causes a profound high bone turnover phenotype similar to human diseases

doi: 10.64898/2026.03.11.709826

Figure Lengend Snippet: Two tibiae from each animal, at 7 weeks of age, were divided into subcortical trabecular-rich bone, bone marrow, and cortical bone (osteocyte-rich bone). Total RNA was isolated and RNAseq was performed on the trabecular-rich area. Three mice per group. (A) Pathway-specific analysis by Gene Ontology for Cellular Components. (B) Pathway-specific analysis by Gene Ontology for Molecular Functions. qRT-PCR was performed and osteoblastic gene expression was measured. (C-F) Trabecular-rich tibial bone: (C) Runx2, (D) Type 1 Collagen (Col1a1), (E) Alkaline Phosphatase (Alpl), and (F) Tnfsf11|Tnfrsf11b (RankllOpg) ratio. (G-J) Osteocyte-rich cortical tibial bone: (G) Runx2, (H) Type 1 Collagen (Col1a1), (I) Alkaline Phosphatase (Alpl), and (J) Tnfsf11|Tnfrs11b (RankllOpg) ratio. Eight to twelve mice per group. Results are means ± SD.

Article Snippet: The RNA-seq libraries were constructed using the Illumina TruSeq Stranded Total RNA library prep kit with Ribozero Gold (San Diego, CA).

Techniques: Isolation, RNA sequencing, Quantitative RT-PCR, Gene Expression