Project description:Primary breast cancer samples were obtained from malignant pleural effusions or ascites after completely red blood cells depletion. For single cell RNA sequencing, frozen vials were thawed and viable breast cancer cells were obtained after depletion of dead cells and CD45+ cells. The purifed patient cells were cultured in Renaissance medium (3D) and treated with chemotherapy (doxorubicin 0.1 µM, carboplatin 0.1mM, paclitaxel 1µM) for 72 hours, and then replaced with Renaissance medium containing DMSO/belinostat (1µM) for 72 hours incubation. The cells were collected, purified with Dead Cell Removal Kit, and subjected to ICELL8® Single-Cell System.
Project description:Purpose: In this study we employed unbiased, genome wide techniques to identify novel enhancers of Sox9 that may cause Disorders of Sex Development (DSDs) when disrupted in the mouse. Methods: We performed ATAC-seq on 60K FACS-purified gonadal cells before and after sex determination to map nucleosome depleted regions (NDRs) indicative of regulatory elements. We then selected 16 putative enhancers present in Sertoli cells. To determine whether these are active enhancers, we performed ChIP-seq for H3K27ac, a histone modification that marks active enhancers. Transient transgenics was performed on select enhancers to determine whether they drive Sertoli-specific expression in vivo. Finally, we selected a single active Sertoli-specific enhancer to delete with CRISPR. Results: We identified a single enhancer upstream of Sox9 that causes complete male-to-female sex reversal in mice when deleted. Conclusions: Our study is the first to identify a single enhacer supstream of Sox9 which drives Sertoli-specific expression in vivo and causes complete male-to-female sex reversal when deleted in the mouse. Furthermore, this enhancer overlaps a region in humans (XY SR) associated to DSDs.
Project description:This SuperSeries is composed of the following subset Series: GSE35911: Reversal of Aberrant Cancer Methylome and Transcriptome upon Direct Reprogramming of Lung Cancer Cells [Expression] GSE35912: Reversal of Aberrant Cancer Methylome and Transcriptome upon Direct Reprogramming of Lung Cancer Cells [Methylation] Refer to individual Series
Project description:T cells are the primary target of the virus HIV-1. Upon infection, the expression of the virus may come to a complete shutdown, a phenomenon known as latency. The molecular mechanisms responsible for the latency of HIV-1 are still poorly understood. To shed light on those mechanisms, we used the J-Lat A2 model for latency reversal, that consists of a Jurkat T cell clone containing a mini HIV construct that is transcriptionally silent. We treated J-Lat A2 and Jurkat cells with the latency-reversing drugs SAHA (suberoylanilide hydroxamic acid) and PMA (phorbol 12-myristate 13-acetate), and we performed single-cell RNA-seq to identify transcriptional signatures shared among the cells where HIV is reactivated.
Project description:we performed single-cell RNA-sequencing by Seq-Well on skin biopsy specimens from five reversal and five lepromatous patients. We obtained 21,318 cells from 10 biopsy specimens, detecting an average of 741 genes and 3,556 transcripts per cell. we recovered 12 primary cell types across all 10 samples. These annotated cell types include: T cells, B cells, plasma cells, myeloid cells, Langerhans cells, mast cells, keratinocytes, fibroblasts, smooth muscle cells, endothelial cells, eccrine gland cells and melanocytes.
Project description:This SuperSeries is composed of the following subset Series:; GSE9504: Expression data from hybrid female Xenopus sex reversal experiment; GSE9505: Expression data from hybrid male Xenopus sex reversal experiment Experiment Overall Design: Refer to individual Series
Project description:This series represents the Cancer Genome Anatomy Project SAGE library collection. Libraries contained herein were either produced through CGAP funding, or donated to CGAP. The Cancer Genome Anatomy Project (CGAP: http://cgap.nci.nih.gov) is an interdisciplinary program established and administered by the National Cancer Institute (NCI: http://www.nci.nih.gov) to generate the information and technological tools needed to decipher the molecular anatomy of the cancer cell. SAGE libraries are named according to the following convention: * SAGE_Organ_histology_code_unique identifier, e.g., SAGE_Colon_adenocarcinoma_CL_Caco2 * Codes: B = bulk; CL = cell line; CS = short-term cell culture; MD = micro-dissected; AP = antibody purified.
Project description:This series represents the Cancer Genome Anatomy Project SAGE library collection. Libraries contained herein were either produced through CGAP funding, or donated to CGAP. The Cancer Genome Anatomy Project (CGAP: http://cgap.nci.nih.gov) is an interdisciplinary program established and administered by the National Cancer Institute (NCI: http://www.nci.nih.gov) to generate the information and technological tools needed to decipher the molecular anatomy of the cancer cell. SAGE libraries are named according to the following convention: * SAGE_Organ_histology_code_unique identifier, e.g., SAGE_Colon_adenocarcinoma_CL_Caco2 * Codes: B = bulk; CL = cell line; CS = short-term cell culture; MD = micro-dissected; AP = antibody purified.