Project description:We performed a detailed analysis of the in vitro differentiation of induced pluripotent stem cells to macrophages and dendritic (chromatin accessibility data).
Project description:This work attempt at characterizing the chromatin accessibility of control and HVDAS lines. We profiled 5 control and 5 HVDAS lines with bulk ATAC-seq, to reconstruct the molecular basis of HVDAS at early stages of development. This data was then integrated with HPTMs and TF ChIP-seq generated from the same lines to identify chromatin accessibility changes connected with ADNP binding changes in HVDAS.
Project description:Probing the role of mechanical oscillations in Hydra regeneration by manipulating environmental osmotic properties. Single spheroids from a period of 22h were collected at 1h intervals and sequenced in both a normal hypotonic medium (HM), as well an isotonic medium (70mM sucrose).
Project description:Zebrafish Primordial Germ Cells (PGCs) were tracked in the Tg(Buc-GFP) line where the germ plasm protein Buc is fused to GFP. GFP-positive cells were isolated via FACS and RNA-seq was performed on polyadenylated transcripts for PGCs and somatic cells at 256-cell, high, dome, 10 somites and prim-5 stages. Two hundred cells were used for each biological replicate.
Project description:NvElav1::mOrange is a stable transgenic line that labels a large fraction of the nervous system of the sea anemone Nematostella vectensis (Nakanishi et al., Development 2012). Two week old primary polyps were dissociated and the NvElav1::mOrange positive cells were enriched by FACS.
Project description:We performed ATAC-seq in v-Abl transformed pro-B cells and its various mutant derivatives to study the differential molecular mechanisms of Igk secondary V(D)J recombination.
Project description:Transposon insertion site sequencing (TIS) is a powerful method for associating genotype to phenotype. However, all TIS methods described to date use short nucleotide sequence reads which cannot uniquely determine the locations of transposon insertions within repeating genomic sequences where the repeat units are longer than the sequence read length. To overcome this limitation, we have developed a TIS method using Oxford Nanopore sequencing technology that generates and uses long nucleotide sequence reads; we have called this method LoRTIS (Long Read Transposon Insertion-site Sequencing). This experiment data contains sequence files generated using Nanopore and Illumina platforms. Biotin1308.fastq.gz and Biotin2508.fastq.gz are fastq files generated from nanopore technology. Rep1-Tn.fastq.gz and Rep1-Tn.fastq.gz are fastq files generated using Illumina platform. In this study, we have compared the efficiency of two methods in identification of transposon insertion sites.
Project description:Primary human hepatocytes treated with 40 compounds (3 concentrations, 0.1xCmax, Cmax and 10xCmax) and vehicle for 7 h. Compounds have different degree of drug-induced liver injury concern. Data for Figure 2 in connected publication.
Project description:HepG2 treated with 40 compounds (3 concentrations, 0.1xCmax, Cmax and 10xCmax) and vehicle for 7 h. Compounds have different degree of drug-induced liver injury concern. Data for Figure 2 in connected publication.