|
| 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).
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| |
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| Overall design |
DamID experiments with Dam fusions to GFP (control) and RPB-6 (RNA polymerases) in sorted embryonic blastomeres, nanopore amplicon sequencing
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| |
|
| Contributor(s) |
Meister P |
| Citation(s) |
33037050 |
| |
| Submission date |
Sep 03, 2020 |
| Last update date |
Oct 30, 2020 |
| Contact name |
Peter Meister |
| E-mail(s) |
peter.meister@unibe.ch
|
| 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 |
| GSM4764492 |
FACS-sorted intestinal embryonic blastomeres DamID RPB-6, replicate 2 |
| GSM4764493 |
FACS-sorted muscle embryonic blastomeres DamID GFP control, replicate 1 |
| GSM4764494 |
FACS-sorted muscle embryonic blastomeres DamID GFP control, replicate 2 |
| GSM4764495 |
FACS-sorted muscle embryonic blastomeres DamID RPB-6, replicate 1 |
| GSM4764496 |
FACS-sorted muscle embryonic blastomeres DamID RPB-6, replicate 2 |
| GSM4764497 |
FACS-sorted Y embryonic Y cells DamID GFP control, replicate 1 |
| GSM4764498 |
FACS-sorted Y embryonic Y cells DamID GFP control, replicate 2 |
| GSM4764499 |
FACS-sorted Y embryonic Y cells DamID RPB-6, replicate 1 |
| GSM4764500 |
FACS-sorted Y embryonic Y cells DamID RPB-6, replicate 2 |
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| This SubSeries is part of SuperSeries: |
| GSE157418 |
Tissue-specific transcription footprinting using RNA PolII DamID (RAPID) in C. elegans |
|
| Relations |
| BioProject |
PRJNA661263 |
| SRA |
SRP279959 |
| 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 |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data provided as supplementary file |
| Processed data are available on Series record |
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