Cell Lines
- Please request the following lines from Coriell:
Parental iPSC line | CRISPR machinery | Inducible transcription factors for differentiation | Coriell link | Publication |
WTC11 | CRISPRi (dCas9-BFP-KRAB) | n/a | https://www.coriell.org/0/Sections/Search/Sample_Detail.aspx?Ref=AICS-0090-391&PgId=166 | We generated this highly characterized line together with the Allen Institute, using the CRISPRi construct described in Tian et al 2019 (PMID 31422865) |
WTC11 | n/a | Ngn2 | https://www.coriell.org/0/Sections/Search/Sample_Detail.aspx?Ref=GM29370&Product=CC | |
WTC11 | CRISPRi (dCas9-BFP-KRAB) | Ngn2 | https://www.coriell.org/0/Sections/Search/Sample_Detail.aspx?Ref=GM29371&Product=CC | Tian et al 2019 (PMID 31422865) |
NCRM5 | CRISPRi (dCas9-BFP-KRAB) | Ngn2 | https://www.coriell.org/0/Sections/Search/Sample_Detail.aspx?Ref=GM29369&Product=CC | Tian et al 2019 (PMID 31422865) |
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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:
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sgRNA to single-cell mappings from Tian et al (2020) Nature Neuroscience
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Seurat object for microglia scRNA-Seq from Dräger et al (2021)
Bioinformatics
- 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
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):
- Gel comb B (1 ladder well, 2 wide wells with wide separator):
- Gel comb C (1 ladder well, 3 wide wells with wide separators):