SnRNA data of Brain section from Parkinson Mouse Model based on inducible expression of human a-syn constructs
Ontology highlight
ABSTRACT: Using 6-months, 16-months, and 24-months old mice of a inducible expression of human a-syn constructs based Parkinson mouse model, we produced a single nucleus RNA dataset by cutting 0mm Bregma to -5mm Bregma. The Chromium 3’ Single Cell Library Kit (10x Genomics) was used and Sequencing was performed on a NovaSeq 6000.
Project description:Native nuclear RNA immunoprecipiatation of the estrogen receptor α (ERα) in exponentially growing MCF-7 for the identification of RNAs linked to the receptor.
Project description:This study used droplet-based snATAC-seq to profile the chromatin accessibility landscape of 91,922 nuclei in the mouse cerebellum across eleven developmental stages, from the beginning of neurogenesis (e10.5) till adulthood (P63). The study included two biological replicates per stage, one from each sex. Cerebelli were dissected as whole or in two halves, nuclei were extracted and profiled using 10x single-cell ATAC reagent kit (v1.0) and a Chromium controller. Libraries were sequenced using paired-reads on Illumina NextSeq 550 and initial data processing was performed using Cellranger ATAC (1.1).
Project description:This study used droplet-based snATAC-seq to profile the chromatin accessibility landscape of 19,204 nuclei in the opossum (Monodelphis domestical) cerebellum across two developmental stages (postnatal day 21 and adult). The study included two biological replicates per stage, one from each sex, and an additional adult sample enriched for white matter. Cerebelli were dissected in two halves, nuclei were extracted from one half and profiled using 10x single-cell ATAC reagent kit (v1.1) and a Chromium controller. The white matter enriched sample was dissected from coronal cerebellum slices. Libraries were sequenced using paired-reads on Illumina NextSeq 550 and initial data processing was performed using Cellranger ATAC (1.1).
Project description:Joint profiling of chromatin accessibility and gene expression from the same single cell provides critical information about cell types in a tissue and cell states during a dynamic process. These emerging multi-omics techniques help the investigation of cell-type resolved gene regulatory mechanisms. Here, we developed in situ SHERRY after ATAC-seq (ISSAAC-seq), a highly sensitive and flexible single cell multi-omics method to interrogate chromatin accessibility and gene expression from the same single cell. We demonstrated that ISSAAC-seq is sensitive and provides high quality data with orders of magnitude more features than existing methods. Using the joint profiles from thousands of nuclei from the mouse cerebral cortex, we uncovered major and rare cell types together with their cell-type specific regulatory elements and expression profiles. Finally, we revealed distinct dynamics and relationships of transcription and chromatin accessibility during an oligodendrocyte maturation trajectory.
Project description:During the past several decades, in vitro fertilization (IVF) has been increasingly used both in animal production and human infertility treatment. Animals derived from in vitro manipulation are occasionally associated with abnormal offspring syndrome (AOS) and other developmental abnormalities. By studying gene expression of in vitro-produced (IVP) embryos/animals, we gain an indicator of how well this procedure mimics the in vivo environment. Most previous studies of this nature have focused on only a few genes at a time or have been limited to studying the pre-implantation stage; thus, a global view of how gene transcription may be influenced by in vitro procedures during fetal development has yet to be ascertained. To this end, we collected liver and placental tissue samples from in vitro-produced and in vivo control bovine fetuses at day 90 and 180 of gestation. We used a bovine 13K oligonucleotide microarray to investigate the transcriptional profiles in both tissues and compared them with those of their age-matched in vivo counterparts. Surprisingly, in both liver and placental tissues, the transcriptional profiles between IVP and control fetuses, at either 90 or 180 days of gestation, were indistinguishable. A total of 879 genes were found to be significantly regulated during liver development from 90 to 180 days of gestation, but there were no gene expression changes in the placental tissue during this developmental period. Quantitative real time RT-PCR on 11 selected genes confirmed these results. Our results have certain implications for IVF technologies, both in agriculture and in human medicine. A total of 18 samples for each tissue type (liver & placenta) was analyzed (8 biological replicates for in vivo-produced fetuses and 10 biological replicates for in vitro ones). Two technical replicates were done for each sample.
Project description:To obtain new insight into the sexual dimorphism of mammalian livers, single-nucleus RNA-seq was performed on the liver samples from two female and two male adult mice. The single-nucleus libraries were generated on the 10X Chromium Next GEM Single Cell 3ʹ platform and sequenced on Illumina NextSeq 550. We used the data to understand the heterogeneity and sex-biased gene expression of liver cell types. The data revealed significant sex differences primarily focused on hepatocytes. Specifically, from the sex-biased genes detected at the bulk tissue level, we observed that male-biased genes are more highly expressed in male hepatocytes, and female-biased genes are more highly expressed in female hepatocytes.
Project description:This dataset consists of ATAC-seq data from human monocytes, monocyte-derived dendritic cells or monocyte-derived macrophages as well as monocyte-derived cells that were subjected to siRNA treatment targeting CTCF or RAD21. In total, it includes 39 samples.
Project description:Approximatively 75% of the genome of S. aureus (“core” genome) are highly conserved between strains, whereas the remaining 25% (“accessory” genome) are composed of variable regions that are mostly composed of mobile genetic elements (MGE), containing virulence and resistance genes. We have developed a composite DNA-microarray (StaphVar Array) which selectively targets 403 genes located on the accessory or core variable genome. Target genes encode antimicrobial resistance factors (35 %), virulence factors (28 %) and adhesins (31%). This microarray was validated with reference strains and used to characterize the genomic DNA of 13 community-acquired methicillin resistant S. aureus (CA-MRSA) strains representative of all the Multilocus Sequence Types (STs) described to date in Belgium. Analysis of gene content of 8 reference strains by the StaphVar Array matched 96 to 99% of the theoretical results. Analysis of CA-MRSA strains showed that 54.4 % of the genes tested were strain-dependent. Strains presented specific exotoxin, enterotoxin, cytolysin and adhesin gene profile by multi-locus sequence typing (MLST) lineage. One exception to these “lineage-specific” gene profile was the variable presence of the Arginin Catabolic Mobile Element (ACME, characteristic of the USA300 clone) within ST8 strains. In conclusion, this novel StaphVar array enables characterization of more than 400 variable resistance and virulence determinants in S. aureus strains. CA-MRSA strains from Belgium displayed extensive diversity in virulence and resistance profile. The presence of the USA 300 clone in our country was confirmed. Although mainly located on MGE, association of virulence genes were highly conserved within strains of the same MLST lineage. CGH microarray was performed on 13 epidemiologically distinct clinical isolates of methicillin resistant S. aureus. S. aureus labeled genomic DNA were hybridized to StaphVar arrays containing 1326 60mer oligonucleotide probes (Eurogentec, Belgium).
Project description:We found histological evidence for increased abundance of iron accumulating cells in association with fibrotic lung, kidney, and heart diseases in mice and humans. We showed that inducing iron accumulation by intratracheal iron delivery in mice is a potent inducer of inflammation, cellular senescence, and fibrosis. The aim of this study has been to understand the single cell dynamics of iron accumulation and the mechanics that link it to in vivo senescence and to fibrogenesis. To get deeper insight into how different cell types respond to iron accumulation, we performed single nuclei RNA sequencing (snRNA-seq) of lungs from mice which received a single intratracheal dose of iron 2 or 6 days prior to analysis, or PBS 6days prior to analysis (control).
Project description:This dataset consists of in situ HiC-seq data from human monocytes, monocyte-derived dendritic cells as well as monocyte-derived cells that were subjected to siRNA treatment targeting CTCF or RAD21. In total, the data set includes 42 samples.