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Series GSE133079 Query DataSets for GSE133079
Status Public on Sep 09, 2019
Title Systematic identification of cell-cell communication networks in the developing brain
Organism Mus musculus
Experiment type Expression profiling by high throughput sequencing
Summary In the current study, we describe Brain-FACS, a method to simultaneously isolate neural, microglial, mural and endothelial cells from the developing brain to more than 94% purity in around 4 hours. Utilising Brain-FACS, we isolate, transcriptionally analyse and build a cell-cell communication map of the mouse brain at embryonic day E14.5. Transcriptomic analyses on FACS-isolated cell populations provide a ~20-fold increase in sensitivity over single single-cell RNA sequencing methods and allow us to bioinformatically identify 1,710 unique ligand-receptor interactions between neural, endothelial, mural and microglial cells including previously unidentified relationships. Together, this study provides a comprehensive map that reveals the richness of communication within the developing brain.
 
Overall design Mouse E14.5 WT and Mof KO brains were dissociated and either mCEL-Seq2 protocol for scRNA-seq or population-based FACS-sorting and bulk RNA-seq was performed.
 
Contributor(s) Sheikh BN, Bondareva O, Aizarani N, Sagar ., Guhathakurta S, Grün D, Hein L, Akhtar A
Citation(s) 31677479
Submission date Jun 20, 2019
Last update date Nov 27, 2019
Contact name Olga Bondareva
Organization name Helmholtz Zentrum München
Department HI-MAG
Street address Philipp-Rosenthal-Straße 27
City Leipzig
State/province Saxony
ZIP/Postal code 04103
Country Germany
 
Platforms (2)
GPL17021 Illumina HiSeq 2500 (Mus musculus)
GPL21493 Illumina HiSeq 3000 (Mus musculus)
Samples (35)
GSM3899460 N-340
GSM3899461 N-343
GSM3899462 N-346
Relations
BioProject PRJNA549887
SRA SRP201993

Download family Format
SOFT formatted family file(s) SOFTHelp
MINiML formatted family file(s) MINiMLHelp
Series Matrix File(s) TXTHelp

Supplementary file Size Download File type/resource
GSE133079_Bulk_norm_counts.txt.gz 1.5 Mb (ftp)(http) TXT
GSE133079_GEO_info_cellbarcodes_cellid.txt.gz 5.5 Kb (ftp)(http) TXT
GSE133079_KO_info_cellbarcodes_cellid.txt.gz 7.3 Kb (ftp)(http) TXT
GSE133079_RAW.tar 8.9 Mb (http)(custom) TAR (of CSV)
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file
Processed data are available on Series record

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