Last updated: 2021-07-23

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Knit directory: neural_scRNAseq/

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Rmd 1755a27 khembach 2021-02-18 plot stathmin2 read coverage of cells from cluster 12
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Rmd e6766a6 khembach 2021-01-28 cluster TDP experiment together with D96 samples
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Rmd 417e7b2 khembach 2021-01-21 cluster TDP-HA samples together with timeline samples
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Rmd 21d8e8c khembach 2020-11-19 find markers for cluster 12
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Rmd 68d329d khembach 2020-11-10 analyse clusters of all timepoints
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Rmd fabdbda khembach 2020-10-29 integrate all time points with the organoid data
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Rmd a528e83 khembach 2020-10-16 cluster analysis TDP experiment
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Rmd 6d7e3c3 khembach 2020-10-15 TDP-43-HA expression in filtered cells
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Rmd e6e6710 khembach 2020-10-15 cluster old samples with D223 sample (no integration)
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Rmd 10a7762 khembach 2020-10-14 include alevin quants for plasmid
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Rmd 55cc8fa khembach 2020-10-12 clustering without integration
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Rmd e5acfd9 khembach 2020-10-07 Cell filtering of TDP experiment
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Rmd 6b39698 khembach 2020-10-07 quality control of TDP experiment
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Rmd d425729 khembach 2020-10-07 preprocessing of new sequencing data
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Rmd f91df7b khembach 2020-09-20 cluster abundances of cell line and stage integration
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Rmd ec8eba6 khembach 2020-09-16 conos analysis with cell line integration
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Rmd dfbc9a8 khembach 2020-09-11 Conos analysis with different parameters and label propagation
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Rmd 043115f khembach 2020-09-02 group organoid integration cluster abundances
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Rmd 638915f khembach 2020-08-14 organoid clustering
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Rmd d8bd339 khembach 2020-07-08 NSC integration with NES from Lam et al.
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Rmd 6d0742b khembach 2020-07-02 wflow_publish(c("analysis/NSC-1-clustering.Rmd", "analysis/NSC-2-annotation.Rmd",
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Rmd f349423 khembach 2020-06-21 regress out number of UMIs and perc mitochondrial features; cyclone
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Rmd 97d5a52 khembach 2020-05-29 cluster analysis
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Rmd 7f5c1f8 khembach 2020-05-29 dimension reduction and clustering
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Rmd a7ced59 khembach 2020-05-28 cell and gene filtering
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Rmd e4c9cd1 khembach 2020-05-22 Start workflowr project.

This analysis includes following steps:

Analysis of the two NSC samples:

Integrated analysis of all 6 samples:

Integration with Lam et al. 2019. Neuroepithelial stem (NES) cells:

Integration with Kanton et al. 2019. Cerebral organoids:

Integration with Conos:

We additionally sequenced neural cultures at 223 days and performed a TDP-43 overexpression experiment (at 96 days):

We quantified the transcript encoded by the plasmid and the endogenous TDP-43 with alevin and include the counts in the analysis.

We combine the TDP-HA samples with the D96 samples as controls (all samples are D96):

TDP-HA samples and all other samples:

We combine the D223 samples with the P22, D56 and D96 samples:

We also integrate the organoid samples:

Test experiment for demultiplexing with hashtag oligos