Resources

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​

• 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 our protocols on protocols.io:
https://www.protocols.io/groups/kampmannlab/publications

Cell Lines

• CRISPRi iPSC line (WTC11 background):
  Obtain a highly characterized line we generated together with the Allen Institute here:
  https://www.coriell.org/0/Sections/Search/Sample_Detail.aspx?Ref=AICS-0090-391&PgId=166

• 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.

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):
  GelCombA.txt
• Gel comb B (1 ladder well, 2 wide wells with wide separator): 
  GelCombB.txt
• Gel comb C (1 ladder well, 3 wide wells with wide separators): 
  GelCombC.txt