作者,Evil Genius
又是新的一周,这周的空气真好。
今天我们来讨论一个关于质控的问题,我们都知道单细胞是需要质控的,去除低质量的细胞、去除双细胞等等,那么空间转录组是否也需要类似的质控分析呢?或者说空间转录组应该如何做质控分析呢?这里我们也参考大量的文献,看看高分文献都是怎么做的。
文献Midkine expression by stem-like tumor cells drives persistence to mTOR inhibition and an immune-suppressive microenvironment
杂志:Nature Communications
时间:2022年8月
样本类型:kidney(癌样本)
空转质控标准:无质控,图片校准之后直接下游分析(直接标准化,降维聚类)
文献Integrated single-cell transcriptomic analyses reveal that GPNMB-high macrophages promote PN-MES transition and impede T cell activation in GBM
杂志:EBioMedicine
时间:2022年9月
样本类型:Glioblastoma
空转质控标准:无质控,图片校准之后直接下游分析(直接标准化,降维聚类)
文献Spatial multi-omic map of human myocardial infarction
杂志:nature
时间: 2022年8月
样本类型 :心脏(心肌梗死样本)
空转质控标准:Spots with less than 300 measured genes and less than 500 UMIs were filtered out. Ribosomal and mitochondrial genes were excluded from this analysis.
文献Spatially resolved clonal copy number alterations in benign and malignant tissue
杂志:nature
时间: 2022年8月
样本类型 :prostates
空转质控标准:removing spots with fewer than 100 genes or transcripts
文献Single-cell and spatial mapping Identify cell types and signaling Networks in the human ureter
杂志:Developmental Cell
时间: 2022年8月
样本类型 :human ureter
空转质控标准:图像校准,无质控(不去除spot),分析的时候对线粒体和红细胞基因的比例进行矫正
文献:Cancer cell states recur across tumor types and form specific interactions with the tumor microenvironment
杂志:Nature Genetics
时间: 2022年8月
样本类型 :癌
空转质控标准:spots with fewer than 500 UMIs or more than 30% mitochondrial or ribosomal reads were filtered out。
文章Single-cell roadmap of human gonadal development
杂志:Nature
时间: 2022年7月
样本类型 :human gonadal
空转质控标准:All spots under tissue detected by Space Ranger were included in downstream analysis.
文章Identification of early neurodegenerative pathways in progressive multiple sclerosis
杂志:Nature Neuroscience
时间: 2022年7月
样本类型 :brain tissue
空转质控标准:Nonprotein-coding genes and ribosomal protein-coding genes were removed, as well as spot transcriptomes consisting of <300 expressed genes. Sampling areas retaining <20 spot transcriptomes meeting the quality criteria were excluded from further analysis.
文章Mesenchymal-epithelial interaction regulates gastrointestinal tract development in mouse embryos
杂志:Cancer Cell
时间: 2022年6月
样本类型 :mouse embryos
空转质控标准:无质控,图片匹配后全部纳入下游分析
文章Spatially resolved multi-omics deciphers bidirectional tumor-host interdependence in glioblastoma
杂志:Cancer Cell
时间: 2022年6月
样本类型 :glioblastoma
空转质控标准:无质控,HE染片全部覆盖的spot纳入下游分析(所有基因)。
文章Cardiac fibroblasts regulate the development of heart failure via Htra3-TGF-β-IGFBP7 axis
杂志:Nature Communications
时间: 2022年6月
样本类型 :heart(mouse)
空转质控标准:无质控,HE染片全部覆盖的spot纳入下游分析(所有基因)。
文章Lymphatics act as a signaling hub to regulate intestinal stem cell activity
杂志:Cell Stem Cell
时间: 2022年6月
样本类型 :heart(mouse)
空转质控标准:无质控,HE染片全部覆盖的spot纳入下游分析(所有基因)。
文章Human distal lung maps and lineage hierarchies reveal a bipotent progenitor
杂志:nature
时间: 2022年4月
样本类型 :Human distal lung
空转质控标准:无质控,HE染片全部覆盖的spot纳入下游分析(所有基因)。
文章Single-cell and spatial analysis reveal interaction of FAP+ fibroblasts and SPP1+ macrophages in colorectal cancer
杂志:Nature Communications
时间: 2022年4月
样本类型 :colorectal cancer
空转质控标准:Spot were filtered for minimum detected gene count of 200 genes while genes with fewer than 10 read counts or expressed in fewer than 3 spots were removed.
文章Spatial CRISPR genomics identifies regulators of the tumor microenvironment
杂志:Cell
时间: 2022年3月
样本类型 :lung and breast tumors
空转质控标准:无质控,HE染片全部覆盖的spot纳入下游分析(所有基因)。
文章The spatial transcriptomic landscape of the healing mouse intestine following damage
杂志:Nature Communications
时间: 2022年2月
样本类型 :mouse intestine
空转质控标准:无质控,HE染片全部覆盖的spot纳入下游分析(所有基因)。
文章Spatial proteogenomics reveals distinct and evolutionarily conserved hepatic macrophage niches
杂志:Cell
时间: 2022年1月
样本类型 :肝(人和小鼠)
空转质控标准:无质控,HE染片全部覆盖的spot纳入下游分析(所有基因)。
文章Mapping the temporal and spatial dynamics of the human endometrium in vivo and in vitro
杂志:Nature Genetics
时间: 2021年12月
样本类型 :子宫内膜
空转质控标准:无质控,HE染片全部覆盖的spot纳入下游分析(所有基因)。