New born neuron marker: Firstly Neurog2 and Tuj1, then NeuroD1 and Tbr2 (Tbr2 is frequently used as new born neuron marker in rodents), then NeuroD2 and Tbr1 (deep layer marker).
The cascade from Hes1 (repress Ascl1 and Neurog1/2. Therefore downregulate Hes1 can induce neural differentiation), Ngn2, Tbr2, Tbr1 is intriguing process swiching fate of stem cell to neuron.
Stab2 repress Ctip2.
Similar to CTIP2, CTIP1 directly represses Tbr1 in layer V and is required for the projection of the corticospinal tract past the pons (Cánovas et al., 2015). Fezf2, Ctip1, and Ctip2 are therefore master regulator genes that are required for the correct specification and formation of the corticospinal tract.
Repression cascade in layer specifc marker.
Ngn2 (Neurog2) induced an upregulation of NeuroD1 expression. As my interpretion, Ngn2 is the fastest marker right after the asymmerical division (newborn neuron marker)
Temporal sequence is Neurog2 (really one peak), then NeuroD1 (no commercial antibody marker) and DCX (alomst the same timing) (Frequently used antibody for detecting newborn neurons)
Emx1, pallial-expressed transcription factor, appear to contribute to numerous telencephalic structures. Frequently used by Emx1-CreERT2 to construct neural progenitor lineage specific expressed mouse line.
For the dorsal determination, firstly the Six3 (earlist), then Pax6 and Emx1/2 and FoxG1
(from https://www.nature.com/articles/nmeth.3629 )
most notably Pax6, Neurogenin2 (Neurog2), Hes1 and Ascl1/Mash1 have roles in controlling neocortical neurogenesis
NeuN (or called Fox-3), neuron marker.
In the neurons, Hes1 has really low expression level. Ascl1 repressed Hes1 (Anti-work)
radial glia cells (SLC1A3), intermediate progenitor cells (EOMES, antother name is TBR2), and excitatory neurons (SLA).
PCNA a marker for cells in early G1 phase and S phase of the cell cycle.
mitotic marker Ki67
progenitors (SOX2), oRGs (HOPX), IPCs (TBR2 / EOMES), newborn neurons (NEUROD6), maturing neurons (SATB2) and inhibitory interneurons (DLX6-AS1，值得一提的是在dorsal cortex中inter neuron一般就是指inhibitory neurons)
Deep layers, especially layer VI and subplate (SP) (TBR1) (looks like the deepest marker)
layers V and VI (CTIP2)
Upper layer neurons, exclusively expressed against deeper layer neurons marker Ctip2 (Satb2)
neurectodermal (Pax6 and Sox1) (Sox1 is neural specific, however Sox2 broadly expressed everywhere even include stem cells), neuroepithelial (N-cad), and neural precursor (Nestin) markers, as well as markers of undifferentiated hESCs (Nanog)
Region specific marker
(such as HOX genes (hindbrain); PAX7 (midbrain); GBX2 (thalamus); NKX2-1 (medial ganglionic eminence) and
FOXG1 (forebrain) (very specific and one candidate for NE indicator since it is not expressed until neuroectoderm starting to translate into NE)
Emx1 (dorsal cortex) (Another candidate for NE indicator, but its expression level is extremely low and recently it is pointed out to also express on stem cells. Currently we believe Emx2 is better for NE indicator)
Auts2 (prefrontal cortex) Nrp2/Fzd9/Prox1 (hippocampus) Nkx2.1 (ventral forebrain, actually the same with medial ganglionic eminence) TTR (choroid plexus) segregated these regions from one another as early as CS13
anterior CNS markers (BF1, Six3, and Otx2) markers of hindbrain / posterior CNS fate (Gbx2, Krox20, PAX2, Isl1 and Hoxb4).
PH3 and BrdU. Evidence of interkinetic nuclear migration
Neural Stem Cell Marker (Nestin, SOX2, Occludin, E Cadherin, Hes1, Notch1)
Nestin neural precursor / Expressed in CNS stem cells, V1 intermediate filament
SOX2 undifferenced ES cells (transcription factor essential for self-renewal)
Occludin identified in epithelial cells as a integral plasma-membrane protein localized at the tight junctions / a NADH oxidizes enzyme
E-cadherin (epithelial cadherin) are a type of cell adhesion molecule that are important in the formation of adherents
Hes1 influences the maintenance of neural stem cells and progenitor cells
Notch1 extracellular domain consisting of multiple epidermal growth factor-like (EGF) repeats / Notch family members play a role in a variety of developmental processes by controlling cell fate decisions.
ZO1 staining of the apical surface
ZEB2 regulator of SMAD signaling that leads to downstream effects on cell-cell junction proteins (apical traits) including OCLN and CDH1 and 2 (EMT effects of ZEB2 during the NE to RG transition)
oRG - hopx
these findings point to a close interaction between cell-cell junctions and apical constriction, both of which are regulated by ZEB2 to drive the change in cell shape that characterizes this newly described transition state
Oct3/4
SSEA-4
