sciCNV: high-throughput paired profiling of transcriptomes and DNA copy number variations at single-cell resolution

计算生物学 生物 基因剂量 转录组 拷贝数变化 基因组 基因 基因表达谱 遗传学 基因表达
作者
Ali Mahdipour–Shirayeh,Natalie Erdmann,Chungyee Leung-Hagesteijn,Rodger E. Tiedemann
出处
期刊:Briefings in Bioinformatics [Oxford University Press]
卷期号:23 (1) 被引量:8
标识
DOI:10.1093/bib/bbab413
摘要

Abstract Chromosome copy number variations (CNVs) are a near-universal feature of cancer; however, their individual effects on cellular function are often incompletely understood. Single-cell ribonucleic acid (RNA) sequencing (scRNA-seq) might be leveraged to reveal the function of intra-clonal CNVs; however, it cannot directly link cellular gene expression to CNVs. Here, we report a high-throughput scRNA-seq analysis pipeline that provides paired CNV profiles and transcriptomes for single cells, enabling exploration of the effects of CNVs on cellular programs. RTAM1 and -2 normalization methods are described, and are shown to improve transcriptome alignment between cells, increasing the sensitivity of scRNA-seq for CNV detection. We also report single-cell inferred chromosomal copy number variation (sciCNV), a tool for inferring single-cell CNVs from scRNA-seq at 19–46 Mb resolution. Comparison of sciCNV with existing RNA-based CNV methods reveals useful advances in sensitivity and specificity. Using sciCNV, we demonstrate that scRNA-seq can be used to examine the cellular effects of cancer CNVs. As an example, sciCNV is used to identify subclonal multiple myeloma (MM) cells with +8q22–24. Studies of the gene expression of intra-clonal MM cells with and without the CNV demonstrate that +8q22–24 upregulates MYC and MYC-target genes, messenger RNA processing and protein synthesis, which is consistent with established models. In conclusion, we provide new tools for scRNA-seq that enable paired profiling of the CNVs and transcriptomes of single cells, facilitating rapid and accurate deconstruction of the effects of cancer CNVs on cellular programming.
最长约 10秒,即可获得该文献文件

科研通智能强力驱动
Strongly Powered by AbleSci AI
更新
大幅提高文件上传限制,最高150M (2024-4-1)

科研通是完全免费的文献互助平台,具备全网最快的应助速度,最高的求助完成率。 对每一个文献求助,科研通都将尽心尽力,给求助人一个满意的交代。
实时播报
wanci应助超级美采纳,获得10
刚刚
PEI完成签到,获得积分10
刚刚
alex完成签到,获得积分10
1秒前
嘟嘟发布了新的文献求助10
2秒前
Dr.Liujun完成签到,获得积分10
2秒前
3秒前
笃定发布了新的文献求助10
4秒前
暴躁的初夏完成签到 ,获得积分10
5秒前
超人爱吃菠菜完成签到,获得积分10
5秒前
思源应助默默毛豆采纳,获得10
6秒前
zbg发布了新的文献求助10
6秒前
7秒前
感动的紊发布了新的文献求助10
8秒前
9秒前
聪明邪欢发布了新的文献求助10
9秒前
奋斗跳跳糖完成签到,获得积分10
10秒前
fanhongpeng完成签到 ,获得积分10
10秒前
11秒前
gzf完成签到 ,获得积分10
11秒前
aa完成签到,获得积分10
11秒前
11秒前
搜集达人应助姚叔采纳,获得10
12秒前
田様应助英俊的念寒采纳,获得10
12秒前
英俊的铭应助哈哈哈哈采纳,获得10
14秒前
14秒前
沙袋发布了新的文献求助50
14秒前
欧阳发布了新的文献求助10
15秒前
呆啊完成签到,获得积分10
15秒前
爱听歌凤灵完成签到,获得积分10
16秒前
万物更始发布了新的文献求助10
17秒前
进击的和尚完成签到,获得积分10
17秒前
ZYC发布了新的文献求助10
17秒前
今后应助虚心醉蝶采纳,获得10
20秒前
21秒前
22秒前
22秒前
上官若男应助科研靓仔采纳,获得10
22秒前
李海平完成签到 ,获得积分10
23秒前
23秒前
晨曦发布了新的文献求助10
23秒前
高分求助中
Sustainability in Tides Chemistry 2800
Kinetics of the Esterification Between 2-[(4-hydroxybutoxy)carbonyl] Benzoic Acid with 1,4-Butanediol: Tetrabutyl Orthotitanate as Catalyst 1000
The Young builders of New china : the visit of the delegation of the WFDY to the Chinese People's Republic 1000
Rechtsphilosophie 1000
Bayesian Models of Cognition:Reverse Engineering the Mind 888
Handbook of Qualitative Cross-Cultural Research Methods 600
Very-high-order BVD Schemes Using β-variable THINC Method 568
热门求助领域 (近24小时)
化学 医学 生物 材料科学 工程类 有机化学 生物化学 物理 内科学 纳米技术 计算机科学 化学工程 复合材料 基因 遗传学 催化作用 物理化学 免疫学 量子力学 细胞生物学
热门帖子
关注 科研通微信公众号,转发送积分 3137308
求助须知:如何正确求助?哪些是违规求助? 2788393
关于积分的说明 7786079
捐赠科研通 2444547
什么是DOI,文献DOI怎么找? 1299936
科研通“疑难数据库(出版商)”最低求助积分说明 625650
版权声明 601023