From 0654f0fab481d98369d26c3db6da0589b26f7905 Mon Sep 17 00:00:00 2001 From: Anthony Date: Tue, 2 Mar 2021 23:05:29 +0100 Subject: [PATCH] Update scRNA-Seq information in the readme --- README.md | 7 +++++++ 1 file changed, 7 insertions(+) diff --git a/README.md b/README.md index e615972..d079f86 100644 --- a/README.md +++ b/README.md @@ -25,8 +25,15 @@ Prerequisites are listed in `enviro.yaml` file. They can be installed using `con The single-cell RNA-Seq data is available at GEO SRA under project number [GSE146773](https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE146773). +The cell cycle phase and FACS intensity data for these ~1,000 cells are contained in the [input folder](https://drive.google.com/file/d/1mdQbYcDPqiTOHeiYbv_4RtrxrmlhYMNl/view?usp=sharing) within the file `ProteinData/WellPlatePhasesLogNormIntensities.csv`: +* The column "Well_Plate" (e.g., A10_355) corresponds to the sample title within GEO SRA (e.g., "Single U2OS cell A10_355"). +* The column "Stage" corresponds to the phase assigned by FACS gating. +* The "Green530" and "Red585" columns correspond to the log-intensities for the red (CDT1) and green (GMNN) FUCCI markers for the individual cells. + The `snakemake` workflow used to analyze the scRNA-Seq dataset, including RNA velocity calculations and louvain unsupervised clustering, can be found in this repository: https://github.com/CellProfiling/FucciSingleCellSeqPipeline. +The `loom` file containing the results of RNA velocity analysis, including spliced and unspliced counts, can be found in the [input folder](https://drive.google.com/file/d/1mdQbYcDPqiTOHeiYbv_4RtrxrmlhYMNl/view?usp=sharing) under `RNAData/a.loom`, and the observation names used for each cell that match the "Well_Plate" identifiers can be found in `RNAData/a.obs_names.csv`. + ## Citation Mahdessian, D.\*; Cesnik, A. J.\*; Gnann, C.; Danielsson, F.; Stenström, L.; Arif, M.; Zhang, C.; Le, T.; Johansson, F.; Shutten, R.; Bäckström, A.; Axelsson, U.; Thul, P.; Cho, N. H.; Carja, O.; Uhlén, M.; Mardinoglu, A.; Stadler, C.; Lindskog, C.; Ayoglu, B.; Leonetti, M. D.; Pontén, F.; Sullivan, D. P.; Lundberg, E. “Spatiotemporal dissection of the cell cycle with single cell proteogenomics.” Nature, 2021, 590, 649–654. \*Contributed equally. https://www.nature.com/articles/s41586-021-03232-9