 |
 |
GEO help: Mouse over screen elements for information. |
|
| Status |
Public on Jun 08, 2024 |
| Title |
Inferring pattern-driving intercellular flows from single-cell transcriptomics of young human cortical organoids |
| Organism |
Homo sapiens |
| Experiment type |
Expression profiling by high throughput sequencing
|
| Summary |
Intercellular communication drives directed flows of information that are mediated by intracellular gene modules, in turn triggering outflows of other signals. Methodologies to describe such intercellular flows are severely lacking. We present FlowSig, a method that infers communication-driven intercellular flows from scRNA-seq using graphical causal modeling and conditional independence. We used human cortical organoid samples collected at D18 and D35 to demonstrate the functions of FlowSig.
|
| |
|
| Overall design |
Organoids were self-assembled using 9,000 stem cells per organoid and cultured in brain cortical region-inducing media. 160 cortical organoids were pooled for a D18 sample, and 25 cortical organoids were pooled for a D35 sample. There were two biological repeats per time point. The samples were subjected to scRNA-seq to identify key signaling pathways from D18 to D35 using FlowSig.
|
| Web link |
https://www.nature.com/articles/s41592-024-02380-w#data-availability
|
| |
|
| Contributor(s) |
Tsai Y, Almet AA, Nie Q, Watanabe M |
| Citation(s) |
39187683 |
| |
| Submission date |
Jul 28, 2023 |
| Last update date |
Sep 07, 2024 |
| Contact name |
Yuan-Chen Tsai |
| E-mail(s) |
yuanct1@uci.edu
|
| Phone |
(949)-824-3429
|
| Organization name |
University of California, Irvine
|
| Department |
Anatomy and Neurobiology
|
| Lab |
Watanabe
|
| Street address |
845 Health Sciences Road
|
| City |
Irvine |
| State/province |
CA |
| ZIP/Postal code |
92697 |
| Country |
USA |
| |
|
| Platforms (1) |
| GPL24676 |
Illumina NovaSeq 6000 (Homo sapiens) |
|
| Samples (1) |
| GSM7667099 |
cortical organoids, D18 and D35, scRNAseq |
|
| Relations |
| BioProject |
PRJNA999674 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSE239542_RAW.tar |
601.2 Mb |
(http)(custom) |
TAR (of CSV, H5AD, MTX, TXT) |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data provided as supplementary file |
|
|
|
|
 |
