Sindhu Lab - Resources

Brain Atlases from other sorces

# https://www.comparativebrainanatomy.org/

# Human Brain Atlas (Developing & Adult)

# Monkey Brain Atlas

# Mouse Brain Atlas

# Zebra Fish Brain Atlas

# Rat Brain Atlas

# Chicken Brain Atlas

# Oppossum Brain Atlas

# Marmoset Brain Atlas

# Lamprey Brain Atlas

Public Database from other labs

# Human Brain scRNA Seq

# Human Organoid scRNA Seq

# Monkey Brain scRNA Seq

# Monkey Brain Organoid scRNA Seq

# Mouse Brain scRNA Seq

# Zebra Fish Brain scRNA Seq

# Zebra Fish Gene Expression Pattern Database

https://zfin.org/

https://mapzebrain.org/home

https://www.ebi.ac.uk/gxa/experiments/E-ERAD-475/Results

https://github.com/U-BDS/zebrafish_telencephalon_atlas

https://www.ezrc.kit.edu/agetaz/

https://ssbd.riken.jp/azebex/

# Rat Brain scRNA Seq

# Chicken Brain sc RNA Seq

# Chicken Brain Gene Expression Pattern Database https://geisha.arizona.edu/

# Oppossum Brain scRNA Seq

# Marmoset Brain scRNA Seq

# Marmoset Gene Expression Database https://gene-atlas.brainminds.jp/

# Lampprey Brain scRNA Seq

# BrainSpan

# Down Syndrome Developmental Brain Transcriptome

# Human Brain Transcriptome

# Non-Human Primate Brain Transcriptome

# Human Brain Genomics

# Mouse Neocortical Transcriptome

# PsychENCODE

^Software

# XSAnno

# Developing cortex transcriptomics (Nowakowski et al. 2017) - UCSC Cell Browser - raw counts matrix

# Developing cortex chromatin accessibility (Ziffra et al. 2021) - UCSC Cell Browser

# Developing thalamus atlas (Kim et al. 2023) - UCSC Cell Browser

# Developmental cell lineage in the cerebral cortex (Keefe, Steyert, et al. 2025) - UCSC Cell Browser

# ASD postmortem tissue - Putamen (Yuan et al. 2025) - UCSC Cell Browser

Protocols (protocols.io)

Wet Lab

# mRNA in situ hybridization

# Stereotaxic Injection in mouse cranium

# in utero/ in ovo electroporation

# AAV production & titre

# RCAS production & titre

# Transgenic mouse production using iGonads

# RNA Scope

# Primary neural culture

# iPSCs & Cell line production

# Brain organoid production

# Mouse/Chick Staging System

# Mouse/Chick/Human/Monkey Brain Atlas

# Sectioning Cryotome or Vibrotome

# Imaging Confocal Microscope & Slide Scanner

# Image data quantification

# Data Storage and retrieval scheme

# DNA cloning : a) RNA probe; b) AAV production c) RCAS production

Dry Lab

# Bulk RNA Seq

# ChIP Seq

# SC RNA Seq

# ATAC Seq

# Cut-&-Run Analysis

# Spatial Seq

# Metabolomic Analysis LCMS

# Multiomics

# GO analysis

# WGCA analysis

# Exome Seq

#Lod score

Plasmids (Addgene)

# Cloning vectors

# in situ probes

# AAVs

# RCAS

Gene Lists

Data Storage

figshare.com (Excel data, Quantification etc.)
Github.com (code storage and sharing)
NCBI (for raw seq files)