Gene Expression Nebulas
基于标准化流程分析的转录图谱综合数据库

Gene Expression Nebulas

多物种转录图谱整合数据库

PRJNA540859: Single-cell transcriptional profiles in human skeletal muscle

来源: NCBI / GSE130646
提交时间: May 02 2019
释放时间: Jan 16 2020
最后更新时间: Jan 16 2020

概要: Skeletal muscle is a complex heterogeneous tissue comprised of diverse muscle fiber and non-fiber cell types that, in addition to movement, influences other systems such as immunity, metabolism and cognition. We investigated gene expression patterns of resident human skeletal muscle cells using single-cell RNA-seq of dissections from vastus lateralis. We generate transcriptome profiles of 11 mononuclear human skeletal muscle mononuclear cell types, including immune, endothelial, pericyte and satellite cells.  We delineate two fibro-adipogenic progenitor cell subtypes that may contribute to heterotopic ossification and muscular dystrophy fibrosis under pathological conditions. An important application of cell type signatures is for computational deconvolution of cell type specific changes using data from bulk transcriptome experiments. Analysis of transcriptome data from a 12 week resistance training study using the human skeletal muscle cell-type signatures revealed significant changes in specific mononuclear cell-type proportions related to age, sex, acute exercise and training. This characterization of human skeletal muscle cell subtypes will resolve cell type specific changes in large-scale physical activity muscle transcriptome studies and can further the understanding of the diverse effects of exercise and the pathophysiology of muscle disease.

项目整体设计: Single cell RNA sequencing was conducted on four samples of mononuclear muscle cells isolated from a single vastus lateralis biopsy.

GEN 数据集:
GEND000118
测序方法:
物种:
组织:
健康状况:
细胞类型:
方案
生长方案: -
处理方案: -
提取方案: Four individual samples of dissociated cryopreserved cells (non-fiber cells only) obtained from a single human muscle biopsy were thawed based on the 10X Genomics Demonstrated Protocol (Manual Part Number CG00039 Rev C). Briefly, cryovials were removed from liquid nitrogen storage and immediately thawed in a 37℃ waterbath for 2 minutes. 1ml of the thawed cells were transferred into individual tubes, the cryovials were rinsed with 1ml of warm complete growth medium and the rinse medium was added dropwise (1 drop per 5 sec) to each tube containing the thawed cells. The cells were serially diluted with complete growth medium a total of 3 times by 1:1 volume dropwise additions with 1 minute wait before each addition. Next the cells were centrifuged at 300 rcf for 5 minutes and resuspended in complete growth medium. Cells were filtered through a 40μm cell strainer, counted, and the volume of medium was adjusted for the final concentration to be 1,000 cells/μl
建库方案: Single-cell encapsulation with beads using the 10X Genomics Chromium Single Cell 3' v2 kit (PN 120235 and PN 120234 Module 1) was performed following manufacturer instructions (User Guide Rev A, 10X Genomics, Pleasanton, CA, USA). Briefly, 4 wells of a 10X microfluidic chip (PN 120236) were loaded each with an individual sample to target 5,000 cells per sample. Single-cell gel beads in emulsion (GEMs) were generated and reverse-transcription was performed in the emulsion prior to 12 cycles of cDNA amplification. Quality control and quantification of the amplified cDNA were assessed by Bioanalyzer. Libraries were constructed according to manufacturer instructions (PN 120234 Module 2). Each library was tagged with a different index for multiplexing (PN 120262) during sequencing. Library quality controls were assessed by Bioanalyzer and quantified by Qubit and quantitative PCR (KAPA Biosystems Quantification for Illumina platforms). Sequencing was performed on an HiSeq 2500 (Illumina, Inc., San Diego, CA) using the following read length: 26 bp Read1 (cell barcode(first 16 nt) + UMI(next 10 nt)), 8 bp i7 index (sample index), and 98 bp Read2 (insert).
测序信息
分子类型: poly(A)+ RNA
库的片段类型: PAIRED
库的链类型: Forward
测序平台: ILLUMINA
测序仪型号: Illumina HiSeq 2500
链特异性: Specific
样本
基本信息:
样本描述:
生物条件:
实验变量:
方案:
测序信息:
质量评估:
数据来源 GEN样本编号 GEN数据集编号 系列编号 项目编号 样本编号 样本名称 生物样本编号 样本访问号 实验访问号 释放时间 提交时间 最后更新时间 物种 种族 族裔 年龄 年龄单位 性别 来源名称 组织 细胞类型 细胞亚型 细胞系 疾病 疾病状态 发育阶段 突变/变异 表型 Condition Detail 生长方案 处理方案 提取方案 建库方案 分子类型 库的片段类型 链特异性 库的链类型 加标(Spike-In) 测序方法 测序平台 测序仪型号 细胞数 测序片段数 碱基数 平均测序片段长度_1 平均测序片段长度_2 唯一比对率 多重比对率 覆盖度
文章
Single-cell transcriptional profiles in human skeletal muscle.
Scientific reports . 2020-01-14 [PMID: 31937892]