概要: A 58 year old female diagnosed with a metastic GI-NET underwent resection of primary tumor as well as several metastatic lesions. We performed scRNA-seq of the primary tumor and one lesion from the liver metastasis to perform comparitive analysis between the primary and metastic tumor compositions.
项目整体设计: scRNAseq was performed on theprimary small intestinal neuroendocrine tumor and its matched liver metastasis simultaneously.
Both primary neuroendocrine tumor and metastatic liver lesion were processed simulatneously, to avoid batch effects. Single cell suspensions were prepared via both mechanical and enzymatic digestion protocols (collagenase I, DNAseI and TrpLE) .Viable cell count was determined using trypan blue exclusion and a total of 10,000 cells per sample were loaded onto the 10X microfluidic chip. mRNA from individual cells were captured and tagged with barcodes using 10X-Genomics microfluidic platform. cDNA was then prepared in the encapsulated gel bead emulsion and the emsulion was broken for further library preparation.
建库方案:
Barcoded cDNA libraries were prepared according to manufacturer's instructions, 10X Genomics.
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 4000
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
Comparative single-cell RNA sequencing (scRNA-seq) reveals liver metastasis-specific targets in a patient with small intestinal neuroendocrine cancer.
Cold Spring Harbor molecular case studies . 2020-04-01 [PMID:
32054662]
