Bioinformatics
Cell theory: 7 main points
All known living things are made up of one or more cells.
All living cells arise from pre-existing cells by division.
The cell is the fundamental unit of structure and function in all living organisms.
The activity of an organism depends on the total activity of independent cells.
Energy flow (metabolism and biochemistry) occurs within cells.
Cells contain DNA which is found specifically in the chromosome and RNA found in the cell nucleus and cytoplasm.
All cells are basically the same in chemical composition in organisms of similar species.
Genotype-Transcription-gene function phenotype
Bulk RNA-seqhttps://www.youtube.com/watch?v=UgslMZ74ums
Cellar heterogeneity reasons for heterogeneity of the cells Morphology & Transcription & the Genome & Proteome , Cellar heterogeneity cellular heterogeneity leads to tumor . For the tumor using PD1 / PDL1 invalid, now based on individual needs using SINGLE the Cell the Analysis , population-based cohort.
single cell analysis challenges have a small amount so require a separation technique may require repeated.
Chinese Professor Tang rich reward
Single cell isolation separation techniques and their characteristics
Limiting dilution The wells after cells were added to the first row of cells in the well, to achieve the purpose of dilution.
Micromanipulation with a pipette to select the cells of interest
LCM fluorescence do Selection .
FACS is flow cytometry, is now mainstream technology, high-throughput sorting. For example, 10X Genomics | Droplet
MACS screening adding beads cells.
10X genomics beads wrapped inside the oil droplets, characterized by a probe consisting of beads: Rl + Barcode ( name ) + the UMI ( the Identify Different an RNA Sequence ) + poly .
Droplet characterized droplets encapsulated cells.
Single cell cDNA amplification i.e. cDNA was amplified in three ways:
1.PCR amplification 2. In vitro transcription amplification 3.phi29 polymerase amplification PMA
Milestone timeline
Analysis workflow：
Imputation : the use of other cell RNA to make up for missing values
Dimensionality reduction methods:
PCA|tSNE|DM：
Analysis software：
Differential expression analysis
Cell subpopulation identification
Cell lineage and state trajectory cell trajectory / linage and pseudotime reconstruction / inference software:
Application such as embryonic development
Human cell atlas of human cells Mapping Project:
Taxonomy: cell types cell types
Histology：cell neighborhood and position
Development ：transitions to differentiated cell types
Physiology and homeosrasis同源性：cycles，transient responses and plastic state
Disease：cells and cellular ecosystem
Mechanism Molecular : intracellular intracellular and inter-cellular circuit
Spatially resolved transcriptomes space transcription: Spatially space
URL: https://www.spatialomics.org/SpatialDB/
ST is plated on the tissue chip, chip to see the expression of the corresponding hole, each point represents a fetch gene in different positions, may correspond to a same measuring gene expression levels in different positions.
Slide-seq is tiled with the tissue on the chip, to see the expression of the corresponding chip hole can be a single cell level.
LCM-f
SeqFISH & MERFISH each point of a cell
Paired-cell sequencing for liver cells
Geo-seq | tomo-seq linear expression profile EG : The embryos are cut into a section, the amount of expression of each segment
Spatial DB collection
Transcription Space Group: Interaction spatial information of each cell and the environment and
LAMP webserver --- Elementary knowledge network knowledge framework:
MOOC : W3Schools Website: https://www.w3cschool.cn/
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