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Series GSE115884 Query DataSets for GSE115884
Status Public on Nov 15, 2018
Title Spatio-temporal m(i)RNA architecture and 3' UTR regulation in the C. elegans germline
Organism Caenorhabditis elegans
Experiment type Expression profiling by high throughput sequencing
Non-coding RNA profiling by high throughput sequencing
Summary In animal germlines, regulation of cell proliferation and differentiation is particularly important but poorly understood. Here, using a cryo-cut approach, we mapped RNA expression along the Caenorhabditis elegans germline and, using mutants, dissected gene regulatory mechanisms that control spatio-temporal expression. We detected, at near single-cell resolution, > 10,000 mRNAs, > 300 miRNAs and numerous unannotated miRNAs. Most RNAs were organized in distinct spatial patterns. Germline-specific miRNAs and their targets were co-localized. Moreover, we observed differential 3’ UTR isoform usage for hundreds of mRNAs. In tumorous gld-2 gld-1 mutants, gene expression was strongly perturbed. In particular, differential 3’ UTR usage was significantly impaired. We propose that PIE-1, a transcriptional repressor, functions to maintain spatial gene expression. Our data also suggest that cpsf-4 and fipp-1 control differential 3’ UTR usage for hundreds of genes. Finally, we constructed a “virtual gonad” enabling “virtual in situ hybridizations” and access to all data (https://shiny.mdc-berlin.de/spacegerm/).
 
Overall design Investigation of the spatio-temporal gene expression in the Caenorhabditis elegans germline using a cryo-based approach and single cell protocols.
 
Contributor(s) Diag A, Schilling M, Klironomos F, Ayoub S, Rajewsky N
Citation(s) 30416012
Submission date Jun 15, 2018
Last update date Jan 27, 2019
Contact name Nikolaus Rajewsky
E-mail(s) rajewsky@mdc-berlin.de
Phone +49 30 9406-2998
Organization name Max Delbrück Center for Molecular Medicine
Department Berlin Institute for Medical Systems Biology
Lab Systems Biology of Gene Regulatory Elements
Street address Robert-Rössle-Straße 10
City Berlin
State/province Berlin
ZIP/Postal code 13125
Country Germany
 
Platforms (3)
GPL18245 Illumina HiSeq 2500 (Caenorhabditis elegans)
GPL19757 Illumina NextSeq 500 (Caenorhabditis elegans)
GPL22765 Illumina HiSeq 4000 (Caenorhabditis elegans)
Samples (97)
GSM3192468 N2_total_100ng_A
GSM3192469 N2_total_200ng_A
GSM3192470 N2_pAp_A1
Relations
BioProject PRJNA476356
SRA SRP150643

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
GSE115884_mRNA_bulk.tsv.gz 15.6 Mb (ftp)(http) TSV
GSE115884_mRNA_slices.tsv.gz 123.0 Mb (ftp)(http) TSV
GSE115884_miRNA_bulk.tsv.gz 169.0 Kb (ftp)(http) TSV
GSE115884_miRNA_slices.tsv.gz 1.1 Mb (ftp)(http) TSV
SRA Run SelectorHelp
Raw data are available in SRA
Processed data are available on Series record

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