Resources

Cell Lines

• Please request the following lines from Coriell:

• To request other cell lines, please use the following request form.

Plasmids

Please request our plasmids through the Kampmann Lab page on Addgene.
Plasmids for 6 transcription factors for microglial differentiation are on the Gan Lab page on Addgene.

CRISPRbrain Data Commons

Datasets

• iNeuron-RNA-Seq, visualization of mRNA levels during Ngn2-driven neuronal differentiation from human iPSCs
  Connor Ludwig, Kampmann Lab (2017).
• https://niacard.shinyapps.io/i3Neuron/, visualization of protein levels during Ngn2-driven neuronal differentiation from human iPSCs
  James Hawrot, NIH (2022).
• AD-brain, visualization and exploration of snRNA-Seq data from human entorhinal cortex and superior frontal gyrus (Alzheimer's Disease and Controls)
  Kun Leng, Kampmann Lab (2020).
  Described in Leng, Li et al (2020).
   
• Datasets related to next-generation shRNA libraries described in Kampmann et al (2015) PNAS
   
• NCBI GEO gene expression data sets related to our publications:
  • Tian, Gachechiladze, Ludwig et al (2019) Neuron: GSE124703
  • Guo et al (2020) Nature: GSE134986
  • Leng, Li et al (2021) Nature Neuroscience: GSE147528
  • Tian et al (2021) Nature Neuroscience: GSE152988
  • Dräger et al (2021): GSE178317
• sgRNA to single-cell mappings from Tian et al (2020) Nature Neuroscience
• Seurat object for microglia scRNA-Seq from Dräger et al (2021)

Bioinformatics​

• Cell profiler pipelines and R notebooks from Ramani, Rose et al (2025) Nature Neuroscience.
  Indigo Rose, Kampmann Lab (2025)
   
• Analysis pipelines from Teter et al (2025) Molecular Psychiatry.
  Olivia Teter, Kampmann Lab (2025)
   
• sgCount, a fast and flexible sgRNA counter for CRISPR screen.
  Noam Teyssier, Kampmann Lab (2023)
   
• CRISPR_screen, a CRISPR screen analysis tool expanding on MAGeCK and MAGeCK-iNC functionality
  Noam Teyssier, Kampmann Lab (2023)
   
• MAGeCK-iNC, a pipeline for the analysis of pooled genetic screens.
  Ruilin Tian, Kampmann Lab (2019)
  Described in Tian et al (2019) Neuron.
   
• AD brain analysis, a pipeline for the analysis of snRNA-Seq data.
  Kun Leng, Kampmann Lab (2020)
  Described in Leng, Li et al (2020) Nature Neuroscience.
   
• Inflammatory Reactive Astrocyte analysis, scripts for master regulator analysis, RNA Seq and CROP-Seq analysis
  Kun Leng, Kampmann Lab (2021)
   
• Microglia analysis, scripts for RNA Seq and CROP-Seq analysis
  Syd Sattler, Kampmann Lab (2021)
   
• Microglial morphology analysis, Cell profiler scripts and example images
  Olivia Teter, Kampmann Lab (2021)
   
• CROP-Seq data analysis pipeline
  Ruilin Tian, Kampmann Lab (2020)
  Described in Tian et al (2021) Nature Neuroscience.
   
• VolcanoPlot, a script to generate volcano plots from sgRNA-level phenotypes
  Ruilin Tian, Kampmann Lab (2019)
   
• Cell Profiler pipeline to segment neuronal morphology (download example images).
  Ruilin Tian, Kampmann Lab (2019)
  Described in Tian et al (2019) Neuron.
   
• CRISPRiaDesign, tools for CRISPRi and CRISPRa sgRNA prediction and machine learning.
  Described in Horlbeck et al (2016) eLife 
   
• CRISPulator, a discrete simulation tool for pooled genetic screens.
  Described in Nagy T and Kampmann M (2017) CRISPulator: a discrete simulation tool for pooled genetic screens. BMC Bioinformatics 18:347
   
• GImap, a suite of bioinformatics tools for the analysis of pooled genetic screens and the construction of genetic interaction maps.
  Based on the quantitative framework we developed: Kampmann M, Bassik MC and Weissman JS (2013) Integrated platform for genome-wide screening and construction of high-density genetic interaction maps in mammalian cells.Proceedings of the National Academy of Sciences 110(25): E2317-26. PMC3690882.

Protocols

Please find the following commonly requested protocols from our lab on protocols.io:

• iPSC culture
• iPSC editing with TALENs
• Neuronal differentiation of iPSCs with stably integrated, inducible Ngn2
• Lentiviral transduction of iPSCs with sgRNAs and sgRNA libraries
• CrAAVE-seq
• AAV production for in vivo CRISPR screens in mouse brains

3D printables

(replace extension with .stl after download)

Gel combs for size fractionation of genomic DNA from pooled screens:

• Gel comb A (1 ladder well, 2 wide wells with narrow separator):

  Document

  GelCombA.txt

• Gel comb B (1 ladder well, 2 wide wells with wide separator): 

  Document

  GelCombB.txt

• Gel comb C (1 ladder well, 3 wide wells with wide separators): 

  Document

  GelCombC.txt