|
| Status |
Public on Mar 30, 2021 |
| Title |
Next Generation Sequencing Facilitates Quantitative Analysis of Wild Type and artificial sweeteners-stressed E. coli K-12 LE392, P. putida KT2440, and RP4 plasmid Transcriptomes |
| Organisms |
Plasmid RP4; Escherichia coli K-12; Pseudomonas putida KT2440 |
| Experiment type |
Expression profiling by high throughput sequencing
|
| Summary |
We report the application of single-molecule-based sequencing technology for high-throughput profiling of histone modifications in mammalian cells. By obtaining over four billion bases of sequence from chromatin immunoprecipitated DNA, we generated genome-wide chromatin-state maps of mouse embryonic stem cells, neural progenitor cells and embryonic fibroblasts. We find that lysine 4 and lysine 27 trimethylation effectively discriminates genes that are expressed, poised for expression, or stably repressed, and therefore reflect cell state and lineage potential. Lysine 36 trimethylation marks primary coding and non-coding transcripts, facilitating gene annotation. Trimethylation of lysine 9 and lysine 20 is detected at satellite, telomeric and active long-terminal repeats, and can spread into proximal unique sequences. Lysine 4 and lysine 9 trimethylation marks imprinting control regions. Finally, we show that chromatin state can be read in an allele-specific manner by using single nucleotide polymorphisms. This study provides a framework for the application of comprehensive chromatin profiling towards characterization of diverse mammalian cell populations.
|
| |
|
| Overall design |
Bacterial mRNA profiles of wild-type E. coli K-12 LE392, P. putida KT2440, and IncPα RP4 plasmid in response to 3 mg/L artificial sweeteners for 2 hours, bacteria and plasmid without dosing artificial sweeteners are the control group, in triplicate, using Illumina HiSeq 2500
|
| |
|
| Contributor(s) |
Yu Z, Wang Y, Lu J, Guo J, Mao L |
| Citation(s) |
33589766 |
| |
| Submission date |
Oct 22, 2019 |
| Last update date |
Jun 30, 2021 |
| Contact name |
Jianhua Guo |
| E-mail(s) |
j.guo@awmc.uq.edu.au
|
| Organization name |
University of Queensland
|
| Department |
Australian Centre for Water and Environmental Biotechnology
|
| Street address |
Research Road, Level 4 Gehrmann Building
|
| City |
Brisbane |
| ZIP/Postal code |
4072 |
| Country |
Australia |
| |
|
| Platforms (1) |
| GPL26609 |
Illumina HiSeq 2500 (Escherichia coli K-12; Plasmid RP4; Pseudomonas putida KT2440) |
|
| Samples (15)
|
|
| Relations |
| BioProject |
PRJNA578873 |
| SRA |
SRP226593 |
Less...
More...