一. 数据预处理

Lane	Exist	1	2	Exist	5	3	4	6	7	8	remark
Day	MEF	D0	D1	D2	D3	D5	D6	D7	D8	ESC
Mapping	ok	ok	ok	ok	ok	ok	ok	ok	ok	ok	ok
Cells	4678	9072	7088	8654	8427	8559	6762	6903	6962	6617
QC	ok	ok	ok	ok	ok	ok	ok	ok	ok	ok	ok
Merge	ok	ok	ok	ok	ok	ok	ok	ok	ok	ok	ok
Trim	ok	ok	ok	ok	ok	ok	ok	ok	ok	ok	ok
Normalization	ok	ok	ok	ok	ok	ok	ok	ok	ok	ok	ok
HVG	ok	ok	ok	ok	ok	ok	ok	ok	ok	ok	ok
rmCC	ok	ok	ok	ok	ok	ok	ok	ok	ok	ok	ok
rm nuisance	ok	ok	ok	ok	ok	ok	ok	ok	ok	ok	ok
remark								test	test	test

事件

2018-4-14 7:38am: 完成mapping
2018-4-14 6:00pm: 完成数据预处理
2018-4-17 20:00 pm: 完成10X数据10000细胞采样的数据作图

备注

Cells: cell number
QC: Filtering low quality cells
Merge: Merge all samples into one matrix
Trim: Trim the extremely gene expression value to avoid outlier effect
Normalization: Normalize by library size
HVG: Find high variable genes
rmCC: Remove cell-cycle annotated genes
rm nuisance: Regress out unwanted factor in data, like nUMI & percent.mito

二. 下游分析

	Main Progress	Testing	Remark
Ifng cells	-	54/7986	Day2
AP clustering	-	ok	用1000个细胞数据做测试
PA & GO enrichment	-	ok	-
Diffusion map	-	ok	-
Force-directed layout	-	ok	-
Show marker genes	-	ok	-

三. C1作图

主图	子图	任务	备注	状态
Figure1	D - tSNE	更新t-SNE，加入D8和iPS		ok
	E - tSNE	更新marker基因图		ok
Figure2	A - SOT	更新t-SNE, 加入D8和iPS		ok
	B - NR/R heatmap	更新热图		ok
	C - SOT	更新marker基因		ok
Figure3	B - TF enrichment	基于新的DEG更新		-
Figure4	B - Last day heatmap	加入D8和MEF/iPS/ESC数据重做		ok
	C- tSNE	基于B挑选的基因重做		ok
Figure6	A - PC/R heatmap	找差异基因重做热图		ok
	B - TF enrichment	基于新的DEG更新		-

10X数据框架图

Figure A (晓山)

10x数据指控图：测序时间点及测序所得细胞数 - 柱状图

Figure B (立惠，源邦)

SOT分支图，以时间作为标注

Figure C (立惠，源邦)

SOT分支图, 聚类结果为标注

Figure D ( (立惠，源邦))

marker基因的表达

 
c("Thy1", "Cdh1", "Epcam", "Cd34", "Klk10", "Fxyd5", "Psca", "Sall4", "Nanog", "Dppa5a")

Figure E (立惠，源邦)

代表分支的cluster的marker基因筛选和GO分析