Journal: BMC Genomics

Article Title: Quantitative analysis of transcriptome dynamics provides novel insights into developmental state transitions

doi: 10.1186/s12864-022-08953-3

Figure Lengend Snippet: Robust BMP Signaling is initiated in Explants Around the Onset of Gastrulation. A Western blot analysis of lysates of developing epidermal (WT) and neural (20uM K02288) explants for pSmad1/5/8 and Smad1 with Actin loading control. Gel was cropped to minimize empty space, uncropped gel is Supplemental Fig. A. B Significance of BMP overrepresentation (hypergeometric p -value) in temporally differentially expressed genes. C-D Graphs of BMP responsive genes in epidermal and neural lineages ( C ) Ventx2.1 ( D ) Id3 . Graphs are sums of S + L allele. Width of the line represents SEM of three biological replicates

Article Snippet: SDS-PAGE and western blot analyses were used to detect proteins and modifications using the following antibodies: anti-phospho SMAD2 (Ser465/467, Sigma, 1:500), Smad2 Polyclonal Antibody (Life Technologies 1:500) Anti-phospho Smad1/Smad5/Smad8 (Ser463/465, Sigma, 1:1000), Smad1 (D59D7, Cell Signal, 1:1000), Actin (A2066, Sigma-Aldrich, 1:5000).

Techniques: Western Blot, Control

Journal: BMC Genomics

Article Title: Quantitative analysis of transcriptome dynamics provides novel insights into developmental state transitions

doi: 10.1186/s12864-022-08953-3

Figure Lengend Snippet: BMP Signaling is Restrained Until stage 10.5 by Dand5 Activity. A-B TPM of genes involved in BMP signaling ( A ) BMP heterodimer ligands BMP7.2, BMP4, BMP2 and primary BMP target Smad, Smad1 ( B ) maternally provided BMP antagonists Dand5 and Gtpbp2 . Graphs are sums of S + L allele. Width of the line represents SEM of three biological replicates. C Western Blot Analysis of lysates for stage 10 epidermal (WT), Dand5 MO injected (40 pmol/embryo), ventral mesoderm (BMP4/7 20 ng/uL), and endoderm (160 ng/uL Activin) explants for pSmad1/5/8 and pSmad2 with Actin loading control. Gels were cropped to minimize empty space, uncropped gel is Supplemental Fig. C. D qRT-PCR of animal pole explants examining the fold change from stage 9 to 13 of expression of mesodermal marker Bra(T) for epidermis(WT), ventral mesoderm(BMP4/7 20 ng/uL) and Dand5 MO(300pmo/embryo) injected(*** P < 0.005)

Article Snippet: SDS-PAGE and western blot analyses were used to detect proteins and modifications using the following antibodies: anti-phospho SMAD2 (Ser465/467, Sigma, 1:500), Smad2 Polyclonal Antibody (Life Technologies 1:500) Anti-phospho Smad1/Smad5/Smad8 (Ser463/465, Sigma, 1:1000), Smad1 (D59D7, Cell Signal, 1:1000), Actin (A2066, Sigma-Aldrich, 1:5000).

Techniques: Activity Assay, Western Blot, Injection, Control, Quantitative RT-PCR, Expressing, Marker

Journal: BMC Genomics

Article Title: Quantitative analysis of transcriptome dynamics provides novel insights into developmental state transitions

doi: 10.1186/s12864-022-08953-3

Figure Lengend Snippet: Early BMP signaling drives ventral mesoderm rather than early epidermal divergence. A Western Blot Analysis of lysates for developing epidermal (WT) and ventral mesoderm (BMP4/7 20 ng/uL) explants for pSmad1/5/8 and Smad1 with Actin loading control. Gel was cropped to minimize empty space, uncropped gel is Supplemental Fig. B. B Number of differentially expressed genes between successive developmental stages of the epidermal and ventral mesoderm lineage, p adj ≤ 0.05. C Venn Diagrams for the total number of DE genes between stages for the epidermal and ventral mesoderm lineages, as well as the number of genes increasing and decreasing over time. D - I TPM of genes representative of different expression dynamics in response to early BMP ( D ) Grhl1 ( E ) Ventx2.1 ( F ) Post ( G ) Vegt (H) Wnt8a ( I ) Mix1 . Graphs are sums of S + L allele. Width of the line represents SEM of three biological replicates

Article Snippet: SDS-PAGE and western blot analyses were used to detect proteins and modifications using the following antibodies: anti-phospho SMAD2 (Ser465/467, Sigma, 1:500), Smad2 Polyclonal Antibody (Life Technologies 1:500) Anti-phospho Smad1/Smad5/Smad8 (Ser463/465, Sigma, 1:1000), Smad1 (D59D7, Cell Signal, 1:1000), Actin (A2066, Sigma-Aldrich, 1:5000).

Techniques: Western Blot, Control, Expressing