From cf3a587a1f62cf83a0ac23acec1f495638a1c8c8 Mon Sep 17 00:00:00 2001 From: samuel-marsh Date: Sat, 22 Jan 2022 15:24:59 -0500 Subject: [PATCH] Update README.md --- README.md | 6 +++--- 1 file changed, 3 insertions(+), 3 deletions(-) diff --git a/README.md b/README.md index 48b899b..9a8cd62 100644 --- a/README.md +++ b/README.md @@ -37,7 +37,7 @@ Included is the code necessary to replicate the Seurat or LIGER (or both) object ## Data ### Original Data -The data in this project can be broadly divided into 2 categories (7 sub-projects). Please see [SI Table 1 & 2](ADD_NEW_LINK) (SI Table 1: Mouse Experiments 1-4) and (SI Table 2; Human Experiments 4-7 & Human Literature Reanalysis) for breakdown by sample, metadata, and more information. +The data in this project can be broadly divided into 2 categories (7 sub-projects). Please see [SI Table 1 & 2](LINK_TBD) (SI Table 1: Mouse Experiments 1-4) and (SI Table 2; Human Experiments 4-7 & Human Literature Reanalysis) for breakdown by sample, metadata, and more information. ***A brief overview with links to the raw data (fastqs) and processed data (Cell Ranger `count` Gene Expression Matrices) see table below*** | Experiment | Species | Seq Used | Description | Raw/Count Data | @@ -52,7 +52,7 @@ The data in this project can be broadly divided into 2 categories (7 sub-project | Exp. 7 | Human | scRNA-seq (10X 5' V1) | scRNA-seq| [*phs002222.v2.p1*](https://www.ncbi.nlm.nih.gov/projects/gap/cgi-bin/study.cgi?study_id=phs002222.v1.p1)| ### Processed Data -All proceesed data files represent the output from Cell Ranger `count`. Files provided are the "*filtered_feature_bc_matrix*" (i.e. only containing the barcodes that Cell Ranger called as cells during preprocessing). Information on Cell Ranger version and Genome/Annotation for each experiment can be found in [SI Table 1 & 2](UPDATE_LINK) as well as individual repository meta data. +All proceesed data files represent the output from Cell Ranger `count`. Files provided are the "*filtered_feature_bc_matrix*" (i.e. only containing the barcodes that Cell Ranger called as cells during preprocessing). Information on Cell Ranger version and Genome/Annotation for each experiment can be found in [SI Table 1 & 2](LINK_TBD) as well as individual repository meta data. **Experiments 1-4, 5 (NCBI GEO)** There are 3 processed data files per library: @@ -88,7 +88,7 @@ Reanalyzed data from literature is summarized detailed in table below. ### Human Data Reanalysis Meta Data Meta data for human data was assembled from published SI Tables, public data on synapse, or restricted access data on synapse - - Compiled publicly available meta data variables for each human dataset can be found in [SI Table 2](UPDATE LINK). + - Compiled publicly available meta data variables for each human dataset can be found in [SI Table 2](LINK_TBD). - "DUC" in the table indicates data available from synapse following submission and approval of Data Use Certificate. ## Acknowledgements: