PROTOCOLS & CODE

PROTOCOLS & CODE

Links to Google Docs or relevant publication

CELL BIOLOGY

Culturing mESCs, including clonal assays
Gene KO with CRISPR/Cas9
Exit from Naïve pluripotency
siRNA transfections
Neural differentiation
Primitive streak-like cell differentiation
Definitive endoderm differentiation
mESC Micropattern Differentiation
Single clone picking, passaging and freezing 96-well plates
Agarose/Fibrin hydrogels (droplets and plates)
Agarose/Fibrin/ECM screen
mESC derivation

MOLECULAR BIOLOGY

Immunostaining cells on plates
Immunostaining mouse embryos (E0-E8.0)
Genomic DNA extraction from 96-well plate
Microcontact printing
Gateway cloning

CODE - BIOINFORMATICS

Analysis of Cut&Tag

CODE - IMAGE ANALYSIS

3D segmentation of agarose/fibrin hydrogel droplets. [Github link]
Quantification and analysis of immunofluorscence. [Github link]
Analysis of live imaging of KTR reporters. [Github link]

External published datasets

A single-cell molecular map of mouse gastrulation and early organogenesis

https://marionilab.cruk.cam.ac.uk/MouseGastrulation2018/

In silico Transcriptomics

http://egastrulation.sibcb.ac.cn

Multi-Omics profiling of early ESC differentiation

http://www.stemcellatlas.org

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