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Series GSE157415 Query DataSets for GSE157415
Status Public on Oct 28, 2020
Title Tissue-specific transcription footprinting using RNA PolII DamID (RAPID) in C. elegans [Blastomeres]
Organism Caenorhabditis elegans
Experiment type Genome binding/occupancy profiling by high throughput sequencing
Summary Gene expression is a major determinant of cell fate and physiology, yet it is notoriously difficult to characterize for the widely used model system C. elegans. By using a new method based on in vivo covalent modification of DNA by RNA polymerases, we determine genome-wide transcription patterns in single tissues of embryos or young adult animals. We show that the method is able to identify actively transcribed genes in tissues representing down to 0.2% of the somatic cells in adult animals. Additionally, this method can be fully performed in a single laboratory by using third generation sequencing methods (ONT).
Overall design DamID experiments with Dam fusions to GFP (control) and RPB-6 (RNA polymerases) in sorted embryonic blastomeres, nanopore amplicon sequencing
Contributor(s) Meister P
Citation(s) 33037050
Submission date Sep 03, 2020
Last update date Oct 30, 2020
Contact name Peter Meister
Phone +41316844609
Organization name University of Bern
Department Institute of Cell Biology
Lab Cell Fate and Nuclear Organization
Street address Baltzerstrasse 4
City Bern
State/province Schweiz
ZIP/Postal code 3012
Country Switzerland
Platforms (1)
GPL26522 MinION (Caenorhabditis elegans)
Samples (12)
GSM4764489 FACS-sorted intestinal embryonic blastomeres DamID GFP control, replicate 1
GSM4764490 FACS-sorted intestinal embryonic blastomeres DamID GFP control, replicate 2
GSM4764491 FACS-sorted intestinal embryonic blastomeres DamID RPB-6, replicate 1
This SubSeries is part of SuperSeries:
GSE157418 Tissue-specific transcription footprinting using RNA PolII DamID (RAPID) in C. elegans
BioProject PRJNA661263
SRA SRP279959

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
GSE157415_Intestine_Muscle_pass_barcode05.genes.details.csv.gz 435.2 Kb (ftp)(http) CSV
GSE157415_Intestine_Muscle_pass_barcode05.sorted_damid-vs-Dam.gatc.bedgraph.gz 3.3 Mb (ftp)(http) BEDGRAPH
GSE157415_Intestine_Muscle_pass_barcode10.genes.details.csv.gz 431.8 Kb (ftp)(http) CSV
GSE157415_Intestine_Muscle_pass_barcode10.sorted_damid-vs-Dam.gatc.bedgraph.gz 3.4 Mb (ftp)(http) BEDGRAPH
GSE157415_Intestine_Muscle_pass_barcode11.genes.details.csv.gz 434.6 Kb (ftp)(http) CSV
GSE157415_Intestine_Muscle_pass_barcode11.sorted_damid-vs-Dam.gatc.bedgraph.gz 3.5 Mb (ftp)(http) BEDGRAPH
GSE157415_Intestine_Muscle_pass_barcode12.genes.details.csv.gz 437.8 Kb (ftp)(http) CSV
GSE157415_Intestine_Muscle_pass_barcode12.sorted_damid-vs-Dam.gatc.bedgraph.gz 3.6 Mb (ftp)(http) BEDGRAPH
GSE157415_RAW.tar 263.5 Mb (http)(custom) TAR (of BAM)
GSE157415_YGR_rpb-6_DamID_pass_barcode01.genes.details.csv.gz 405.4 Kb (ftp)(http) CSV
GSE157415_YGR_rpb-6_DamID_pass_barcode01.sorted_damid-vs-Dam.gatc.bedgraph.gz 2.8 Mb (ftp)(http) BEDGRAPH
GSE157415_YGR_rpb-6_DamID_pass_barcode04.genes.details.csv.gz 421.3 Kb (ftp)(http) CSV
GSE157415_YGR_rpb-6_DamID_pass_barcode04.sorted_damid-vs-Dam.gatc.bedgraph.gz 3.1 Mb (ftp)(http) BEDGRAPH
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Raw data are available in SRA
Processed data provided as supplementary file
Processed data are available on Series record

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