|
| Status |
Public on Oct 28, 2020 |
| Title |
Tissue-specific transcription footprinting using RNA PolII DamID (RAPID) in C. elegans [Young adult] |
| 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 whole animals or specific tissues in young adults C. elegans worms, nanopore amplicon sequencing
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| |
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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 |
| |
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| Platforms (1) |
| GPL26522 |
MinION (Caenorhabditis elegans) |
|
| Samples (16)
|
| GSM4764501 |
Young adults purified DNA intestine-specific DamID GFP control, replicate 1 |
| GSM4764502 |
Young adults purified DNA intestine-specific DamID GFP control, replicate 2 |
| GSM4764503 |
Young adults purified DNA intestine-specific DamID RPB-6, replicate 1 |
| GSM4764504 |
Young adults purified DNA intestine-specific DamID RPB-6, replicate 2 |
| GSM4764505 |
Young adults purified DNA muscle-specific DamID GFP control, replicate 1 |
| GSM4764506 |
Young adults purified DNA muscle-specific DamID GFP control, replicate 2 |
| GSM4764507 |
Young adults purified DNA muscle-specific DamID RPB-6, replicate 1 |
| GSM4764508 |
Young adults purified DNA muscle-specific DamID RPB-6, replicate 2 |
| GSM4764509 |
Young adults purified DNA XXX-specific DamID GFP control, replicate 1 |
| GSM4764510 |
Young adults purified DNA XXX-specific DamID GFP control, replicate 2 |
| GSM4764511 |
Young adults purified DNA XXX-specific DamID RPB-6, replicate 1 |
| GSM4764512 |
Young adults purified DNA XXX-specific DamID RPB-6, replicate 2 |
| GSM4764513 |
Young adults purified DNA worm-wide DamID GFP control, replicate 1 |
| GSM4764514 |
Young adults purified DNA worm-wide DamID GFP control, replicate 2 |
| GSM4764515 |
Young adults purified DNA worm-wide DamID RPB-6, replicate 1 |
| GSM4764516 |
Young adults purified DNA worm-wide 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 |
PRJNA661264 |
| SRA |
SRP279960 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSE157416_Intestine_DamID_2_pass_barcode05.genes.details.csv.gz |
430.7 Kb |
(ftp)(http) |
CSV |
| GSE157416_Intestine_DamID_2_pass_barcode05.sorted_damid-vs-Dam.gatc.bedgraph.gz |
3.1 Mb |
(ftp)(http) |
BEDGRAPH |
| GSE157416_Intestine_DamID_2_pass_barcode11.genes.details.csv.gz |
429.6 Kb |
(ftp)(http) |
CSV |
| GSE157416_Intestine_DamID_2_pass_barcode11.sorted_damid-vs-Dam.gatc.bedgraph.gz |
3.0 Mb |
(ftp)(http) |
BEDGRAPH |
| GSE157416_Muscle_DamID_pass_barcode09.genes.details.csv.gz |
431.1 Kb |
(ftp)(http) |
CSV |
| GSE157416_Muscle_DamID_pass_barcode09.sorted_damid-vs-Dam.gatc.bedgraph.gz |
3.4 Mb |
(ftp)(http) |
BEDGRAPH |
| GSE157416_Muscle_DamID_pass_barcode12.genes.details.csv.gz |
433.1 Kb |
(ftp)(http) |
CSV |
| GSE157416_Muscle_DamID_pass_barcode12.sorted_damid-vs-Dam.gatc.bedgraph.gz |
3.5 Mb |
(ftp)(http) |
BEDGRAPH |
| GSE157416_RAW.tar |
484.3 Mb |
(http)(custom) |
TAR (of BAM) |
| GSE157416_Worm_Wide_Starved_pass_barcode02.genes.details.csv.gz |
430.2 Kb |
(ftp)(http) |
CSV |
| GSE157416_Worm_Wide_Starved_pass_barcode02.sorted_damid-vs-Dam.gatc.bedgraph.gz |
3.2 Mb |
(ftp)(http) |
BEDGRAPH |
| GSE157416_Worm_Wide_Starved_pass_barcode05.genes.details.csv.gz |
422.5 Kb |
(ftp)(http) |
CSV |
| GSE157416_Worm_Wide_Starved_pass_barcode05.sorted_damid-vs-Dam.gatc.bedgraph.gz |
3.0 Mb |
(ftp)(http) |
BEDGRAPH |
| GSE157416_XXX_DamID_pass_barcode07.genes.details.csv.gz |
433.9 Kb |
(ftp)(http) |
CSV |
| GSE157416_XXX_DamID_pass_barcode07.sorted_damid-vs-Dam.gatc.bedgraph.gz |
3.3 Mb |
(ftp)(http) |
BEDGRAPH |
| GSE157416_XXX_DamID_pass_barcode10.genes.details.csv.gz |
427.1 Kb |
(ftp)(http) |
CSV |
| GSE157416_XXX_DamID_pass_barcode10.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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