Project description:Gene expression profiling was performed using the total RNA isolated from pooled esophagi (plural of esophagus) of embryonic day 15.5 (E15.5) C57BL/6 mouse embryos and total RNA isolated from pooled esophagi of postnatal day 2 (P2) C57BL/6 pups. The goal was to identify differentially regulated genes in these two separate developmental stages.
Project description:mRNA transcript levels in embryonic day 15.5 (E15.5), E17.5 and postnatal day 1 (P1) mouse Crb1KOCrb2ΔRPC against mouse Crb1KO neuroretina (Run1), and in E15.5 mouse Crb1KOCrb2ΔRPC against wild type neuroretina (Run2) were analyzed. A comparison between Crb1KOCrb2ΔRPC and Crb1KO retina, at E15.5, or E17.5, or P1 on 100% C57BL/6JOlaHsd, yielded only subtle persistent changes at the transcriptional level over time (Figure 1 G-I, respectively), despite significant differences in morphology. As inter-nal positive control at E15.5, E17.5 and P1 we used ATP-binding cassette, sub-family D (ALD), member 4 (Abcd4), which is substantially upregulated in mouse retina expressing the Cre recombinase fused to the Chx10 promoter, with the Abcd4 gene immediately adja-cent to the Chx10Cre locus in the mouse genome. To further examine potential transcriptional changes at E15.5, we compared Crb1KOCrb2ΔRPC mice in 100% C57BL/6JOlaHsd genetic background against wild type C57BL/6JRccHsd mice. In this setting, we observed 40 differentially expressed genes (DEGs) compared to the previously 0 DEGs (E15.5; adj. p-val < 0.01 & log2FC > 1.5). The Crb1KOCrb2ΔRPC mice on C57BL/6JOlaHsd genetic background, due to mutations in the synuclein alpha (Snca), multimerin-1 (Mmrn1), and Crb1 gene, do not express Snca, Mmrn1, or Crb1 gene transcripts, and express high levels of Abcd4 due to the adjacent Chx10Cre transgene on chromosome 6. We made use of all 4 genes as negative and positive controls in the gene expression profiling, since the mice on C57BL/6JRccHsd genetic background have no mutations in Snca, Mmrn1 or Crb1 and express low levels of Abcd4. Analysis of the E15.5 data revealed upregulated expression of the WD repeat and FYVE domain-containing protein 1 (Wdfy1) gene also known as FYVE domain-containing pro-tein localized to endosomes (Fens-1), which encodes a phosphatidylinositol 3-phosphate binding protein that contains a FYVE zinc finger domain and multiple WD-40 repeat do-mains.
Project description:We collected 3 replicates of whole stomach organs at 15 time points that covered embryonic days (E12.5, E13.5, E14.5, E15.5, E16.5, E17.5, E18.5), postnatal days (D1, D3, D5), and postnatal weeks (W1, W2, W3, W6, W8). The sampling time window covered from the earliest day that stomach sampling is anatomically feasible to the latest weeks when stomachs are close to mature. We applied a fast-seq proteomics workflow, a label-free quantitative proteomics approach in combination with small scale reverse phase pre-fractionation strategy.
Project description:The cerebral cortex plays an important role in cognitive function and specialized perception in mammals and its development requires highly specific spatio-temporal control of gene expression. The study identified stage- and region-specific markers throughout cerebral corticogenesis at various important stages of cerebral cortex development; embryonic day (E) 15.5, E17.5, postnatal day (P) 1.5 and 4-6 months old. The study involved the analysis of 12 SAGE libraries, which were generated from the mouse cerebral cortex of E15.5 (n=3), E17.5 (n=2), P1.5 (n=1) and 4-6 month old (n=6). N denotes biological replicates.
Project description:Purpose: We labeled synchronous cohorts of prenatal and postnatal glutamatergic progenitors to study their lineage relationship and transcriptional specificities. Method and results: We performed scRNA-seq of postnatal glutamatergic progenitors isolated from microdissected pallium at E15.5 or dorsal subventricular zone at P2 in the mouse. Our results highlight transcriptional dysregulation at P2 which includes genes involved in metabolism, differentition and migration.
Project description:To determine changes in pancreatic mesenchymal cells during embryonic development, we analyzed the transcriptome of these cells at three embryonic days: 13.5 ('L1'), 15.5 ('L2'), and 17.5 ('L3'). Pancreatic mesenchymal cells were isolated by FACS from Nkx3.2-Cre;LSL-YFP pancreatic tissues based on these cells fluorescent labeling. Two groups of mice were analyzed for each embryonic day ('P1', 'P2').
Project description:To investigate the transcriptome changes in embryonic and postnatal mouse hearts, we performed gene expression profiling analysis using data obtained from RNA-seq of C57BL/6J mouse hearts at embryonic day 18.5 (E18.5d), postnatal 1st day (P1d) and postnatal 7th day (P7d).
Project description:We report the quantification of steady-state mRNA coding for ribosomal proteins, translation-associated proteins, and Ebp1 (Pa2g4) in mouse total neocortex brain lysates at embryonic days 12.5, 14, 15.5, 17 and postnatal day 0
