PROTOCOLS

PROTOCOLS

• Tole lab in situ hybridization protocol for tissue sections 

• Preserving the pineal gland in perinatal mouse brain preparations 

• Organotypic Explants of the Embryonic Rodent Hippocampus

• Gene Perturbation in Embryonic Hippocampal Progenitors Using Ex Vivo Electroporation Followed by In Vitro Dissociated Cell Culture

DATASETS 

• Brain Atlas of Developmental Gene Expression (BADGE)
  Type of dataset: images
  Description: This platform contains images of gene expression in the developing mouse forebrain generated in the Tole lab using an optimized non-radioactive in situ hybridization. The database contains mouse brain sections across a range of gestational and postnatal stages in the coronal plane, and includes wild-type as well as mutant backgrounds. Mutants include brain sections from standard knockout mice (sKO) and conditional knockout mice (cKO) crossed to different Cre drivers.
  
  

• Publication: Pal et al., 2021

An Early Cortical Progenitor-Specific Mechanism Regulates Thalamocortical Innervation

Type of dataset: Bulk RNA sequencing

Tissue: Microdissected subplate from P0 mouse brain sections 

Genotypes: (a) Control (b) Emx1Cre11.5::Lhx2lox/lox (c) NexCre::Lhx2lox/lox

NCBI GEO: GSE159006

• Publication: Parichha et al., 2022

Constitutive activation of canonical Wnt signaling disrupts choroid plexus epithelial fate

Type of Dataset: Bulk RNA sequencing

Tissue: Choroid plexus and hippocampus of Embryonic day 14.5 mouse embryo

Genotypes: (a) Control (b) Lmx1aCre::β-catenin GOF 

NCBI GEO: GSE162784

• Publication: Suresh et al., 2023

Regulation of chromatin accessibility and gene expression in the developing hippocampal primordium by LIM-HD transcription factor LHX2

Type of Dataset: Bulk RNA sequencing, ATAC seq, LHX2-ChIP seq, Histone-ChIPseq for H3K27Ac, H3K27Me3 andH3K4Me3

Tissue: Hippocampal and Neocortical primodia (Hcp and Ncp respectively) from E12.5 mouse embryos.

Genotypes: (a) Control (b) Emx1Cre11.5::Lhx2lox/lox

Bioproject: PRJNA882662 and PRJNA883170 

• Publication: Bose et al., 2025a

LHX2 regulates dendritic morphogenesis in layer II/III neurons of the neocortex

Type of Dataset: Bulk RNA sequencing

Tissue: GFP was electroporated at E15.5 to target the somatosensory cortex. The electroporated region was microdissected from postnatal day 5 tissue sectioned on a tissue chopper  

Genotypes: (a) Control electroporated with TdT + CAAX EGFP (b) Lhx2lox/lox  electroporated with CreTdT + CAAX EGFP (c) NexCre::Lhx2lox/lox electroporated with CAAX-EGFP 

NCBI GEO : GSE253914

• Publication: Bose et al., 2025b

Dual role of FOXG1 in regulating gliogenesis in the developing neocortex via the FGF signalling pathway

Type of Dataset: Bulk RNA sequencing

Tissue: FACS sorted FOXG1 loss of function mutant in progenitors (mutation at E15.5, collection at E17.5) and post-mitotic neurons (P1) along with corresponding controls.

Genotypes: (a) controls (b) hGFAPCreERT2/+::Foxg1lox/lox:: Ai9/ (c) NexCre/+::Foxg1lox/lox:: FRT-GFP 

NCBI GEO : GSE253919

• Publication: Iyer et al., 2025

The transcription factor LHX2 suppresses astrocyte proliferation in the postnatal mammalian cerebral cortex

Type of Dataset: Bulk RNA sequencing

Tissue: FACS sorted control and Lhx2 mutant mouse cortical astrocytes from P3 mouse pups. 

Genotypes: (a) hGFAPCreERT2/+::Ai9/Ai9 (b) hGFAPCreERT2/+::Lhx2lox/lox::Ai9/Ai9

NCBI Bioproject: PRJNA1149579  

• Publication: Singh et al., 2026

Cajal-Retzius fate specification is disrupted by constitutive activation of β-Catenin in hem progenitors

Type of Dataset: Single cell RNA sequencing 

Tissue: Telencephalic midline tissue from E11.5 and E14.5 mouse embryos. The cortical hem and part of the adjacent hippocampal primordium was dissected.

Genotypes: (a) Lmx1aCre::Ai9 (b) Lmx1aCre::Ai9::β-catenin GOF 

NCBI GEO: GSE273962