Project description:ATAC-seq and RNA-seq were used to compare the chromatin states and corresponding transcriptomes of developing HSPC. We found that the chromatin states and transcriptomes change markedly when HSPCs migrate from PL to FL and from FL to BM. Then we compared chromatin among E12.5 PL, E12.5 FL, and E16.5 FL, the proportion of fragments in the nucleosome-free region significantly increases in E12.5 and E16.5 FL-HSPCs compared with E12.5 PL-HSPCs; the motifs of ETS and Runt are enriched at the opeing or closing peaks from E12.5 PL to E12.5 FL and E12.5 FL to E16.5 FL, and the expression of these factors is either up-regulated or down-regulated; the motifs of bZIP and Zf are enriched at the closing and opening peaks from E12.5 PL to E12.5 FL and E12.5 FL to E16.5 FL respectively, In line, the expression of these factors is down-regulated or up-regulated.
Project description:HOXA7 regulates FL-HSPC self-renewal in vitro and in vivo. We profiled FL-HSPCs after HOXA7 knockdown, to assess the gene expression programs regulated by HOXA7.
Project description:Single-nucleus RNA sequencing (snRNA-seq) was used to profile the transcriptome of 16,015 nuclei in human adult testis. This dataset includes five samples from two different individuals. This dataset is part of a larger evolutionary study of adult testis at the single-nucleus level (97,521 single-nuclei in total) across mammals including 10 representatives of the three main mammalian lineages: human, chimpanzee, bonobo, gorilla, gibbon, rhesus macaque, marmoset, mouse (placental mammals); grey short-tailed opossum (marsupials); and platypus (egg-laying monotremes). Corresponding data were generated for a bird (red junglefowl, the progenitor of domestic chicken), to be used as an evolutionary outgroup.
Project description:Gene expression profiling of immortalized human mesenchymal stem cells with hTERT/E6/E7 transfected MSCs. hTERT may change gene expression in MSCs. Goal was to determine the gene expressions of immortalized MSCs.
Project description:RNA-sequencing (RNA-Seq) protocols and bioinformatic pipelines are designed to streamline downstream analyses on sequences believed to be the most important. Here, we have challenged this dogma by preserving ribosomal RNA (rRNA) in our samples and by lowering the minimal RNA size window of our small RNA-Seq analyses to 8 nt
Project description:ATAC-seq and RNA-seq were used to compare the chromatin states and corresponding transcriptomes of developing HSPC. We found that the chromatin states and transcriptomes change markedly when HSPCs migrate from PL to FL and from FL to BM. Then we compared chromatin among E12.5 PL, E12.5 FL, and E16.5 FL, the proportion of fragments in the nucleosome-free region significantly increases in E12.5 and E16.5 FL-HSPCs compared with E12.5 PL-HSPCs; the motifs of ETS and Runt are enriched at the opeing or closing peaks from E12.5 PL to E12.5 FL and E12.5 FL to E16.5 FL, and the expression of these factors is either up-regulated or down-regulated; the motifs of bZIP and Zf are enriched at the closing and opening peaks from E12.5 PL to E12.5 FL and E12.5 FL to E16.5 FL respectively, In line, the expression of these factors is down-regulated or up-regulated.
