Project description:This dataset contains single nucleus Assay for Transposase-Accessible Chromatin (ATAC) sequencing results from rat nucleus accumbens tissue. Rats received repeated cocaine injections (20mg/kg, intraperitoneal injection), or saline injections as a control. Single-nucleus ATAC-seq was carried out with FACS-sorted nuclei using the 10X Genomics Chromium single cell sequencing platform using the Chromium Next GEM Single Cell ATAC Kit v2.
Project description:This experiment contains two mice genotypes – WT and Bcl3 flx/flx Zbtb46 cre knockouts (both C57BL/6 background). These mice were either infected with 15 cysts of Toxoplasma gondii (ME49 strain) or kept uninfected. Spleens were harvested from mice 7 days post infection and splenocytes were isolated. With four experimental groups (KO/WT and infected/uninfected) and two biological replicate mice per group, we have a total of 8 biological samples comprising of single cell suspensions of splenocytes enriched for CD11c. Single cell RNA-seq libraries were prepared from CD11c-enriched single cells using the Chromium Single Cell 3’ Reagent Kits v3 (10X Genomics; Pleasanton, CA, USA). Eight sample libraries were multiplexed and sequenced 100bp paired end in four different runs of Illumina NextSeq2000, followed by demultiplexing that resulted in multiple raw FASTQ files corresponding to paired reads (R1 and R2), index barcodes (I1) and four sequencing runs (Seq1 - Seq4). The main goal of this project was to define Bcl3-associated transcriptional responses in dendritic cells during T. gondii infection.
Project description:This dataset contains single-nucleus RNA sequencing results from adult rat brain (ventral tegmenal area, or VTA). The goal of this experiment was to define the transcriptional landscapes of distinct cell types in the VTA. Single-cell sequencing was carried out with nuclei suspensions (sorted using flow cytometry) using the 10X Genomics Chromium single cell sequencing platform.
Project description:The adult healthy human pancreas has been poorly studied given lack of indication to obtain tissue from the pancreas in the absence of disease and rapid postmortem degradation. We obtained pancreata from brain dead donors thus avoiding any warm ischemia time. We found that neoplastic lesions occur frequently in healthy organs, in donors as young as in their 3rd decade of life. Using the 10X Genomics Platform, we performed single cell RNA sequencing on 6 donor pancreata, 5 of which we separately sequenced tissue from the pancreas head and tail, for a total of 11 sequencing runs. This is a robust single-cell dataset of healthy, nonpathologic pancreas tissue and includes acinar, ductal, and non-epithelial cells (myeloid cells, fibroblasts, endothelial cells, lymphocytes). We compared this dataset of normal pancreata to single cell sequencing of tumor samples previously published in Steele, et al, Nature Cancer 2020, (raw fastq in dbGap phs002071) realigned to GRCh38 reference genome (CellRanger 6.0). This GEO series contains the raw and filtered feature matrices for the donor pancreata as well as the realigned tumor samples. Supplementary files contain the aggregate feature matrices and the metadata of the donor pancreata samples and the tumor samples.
Project description:This dataset contains single-nucleus RNA sequencing results from adult rat brain (nucleus accumbens) and serves as the basis for characterization of transcriptional response to cocaine (20mg/kg, intraperitoneal injection). The goal of this experiment was to define the transcriptional response to cocaine across distinct cell types in the nucleus accumbens. Single-cell sequencing was carried out on FACS-sorted nuclei isolated from these experiments using the 10X Genomics Chromium single cell sequencing platform.
Project description:This dataset contains single-nucleus RNA sequencing results from adult rat brain (nucleus accumbens) and serves as the basis for characterization of transcriptional response to repeated cocaine injections (20mg/kg, intraperitoneal injection). The goal of this experiment was to define the transcriptional response to repeated cocaine across distinct cell types in the nucleus accumbens. Single-cell sequencing was carried out with FACS-sorted nuclei isolated from these experiments using the 10X Genomics Chromium single cell sequencing platform.
Project description:This study used snATAC-seq to profile Chromatin accessibility in 26 day-old iPSC-derived kidney organoids, treated with TGFB1, the EzH2 inhibitor GSK343, a combination of both or a vehicle control for 48 hours (days 24-26) before harvesting. 2 organoids per condition were pooled and dissociated using a cold-active protease. Nuclei were extracted and profiled using the 10X Genomics Single-cell ATAC reagent kit v1.1. Libraries were sequenced using paired-end reads on an Illumina NovaSeq 6000. Initial processing was performed using CellRanger ATAC v1.2.0 (10X Genomics).
Project description:This dataset contains single-nucleus RNA sequencing results from rat embryonic striatal neuronal cultures and serves as the basis for characterization of transcriptional response to dopamine (50µM), the Drd1 agonist SKF-38393 (1µM), and potassium chloride (25mM). The goal of this experiment was to define the transcriptional response to each of these stimulations across distinct cell types in cultured neurons. Single-cell sequencing was carried out on FACS-sorted nuclei isolated from these experiments using the 10X Genomics Chromium single cell sequencing platform.