|
| Status |
Public on Jul 31, 2021 |
| Title |
sigC-deletion CapSeq 6h |
| Sample type |
SRA |
| |
|
| Source name |
N. punctiforme
|
| Organism |
Nostoc punctiforme PCC 73102 |
| Characteristics |
strain/genotype: ATCC 29133; sigC-deletion
filament type: developing hormogonia
time following hormogonium induction: 6 h
molecule subtype: 5'-Triphosphorylated RNA
|
| Treatment protocol |
For hormogonium induction, culutres were harvested at 1000xg for 5 min, washed 3x with AA/4 to remove sucralose, and resuspended in AA/4 without sucralose
|
| Growth protocol |
Nostoc punctiforme strains were cultured in Allan and Arnon medium diluted four fould (AA/4), in the absence of a source of fixed nitrogen, as previously described (Campbell et al. 2007. Global gene expression patterns of Nostoc punctiforme in steady-state dinitrogen-grown heterocyst containing cultures and at single time points during the differentiation of akinetes and hormogonia. J. Bacteriol 189:5247-5256) with the exception that cultures were supplemented with 4 mM sucralose to suppress hormognium development prior to induction as previously described (Splitt and Risser, 2016. The non-metabolizable sucrose analog sucralose is a potent inhibitor of hormogonium differentiation in the filamentous cyanobacterium Nostoc punctiforme. Arch Microbiol. 2016 Mar;198(2):137-47)
|
| Extracted molecule |
total RNA |
| Extraction protocol |
RNA extractions were performed as previously described with a bead beater and phenol (Campbell et al. 2007. Global gene expression patterns of Nostoc punctiforme in steady-state dinitrogen-grown heterocyst containing cultures and at single time points during the differentiation of akinetes and hormogonia. J. Bacteriol 189:5247-5256)
Total RNA was used to generate libraries for Cappable-seq as previously described (Ettwiller et. al., BMC Genomics volume 17, Article number: 199 (2016)) by Vertis Biotechnologie AG
|
| |
|
| Library strategy |
OTHER |
| Library source |
transcriptomic |
| Library selection |
other |
| Instrument model |
Illumina NextSeq 500 |
| |
|
| Data processing |
library strategy: Cappable-seq
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence at Vertis Biotechnologie AG prior to dissemination of data to the end user
The reads were mapped to the N. punctiforme genome using Bowtie2 local
TSSs were defined in the wild type strain using the following programs: bam2firstbasegtf.pl cutoff 1; cluster_tss.pl cutoff 5 (https://github.com/Ettwiller/TSS/)
Quantitation of TSSs in the sigma factor deletion strains was performed by running bam2firstbasegtf.pl cutoff 1 for each of the mutant strain libraries, and then retrieving the relative read score (RRS) at the position corresponding to each TSS defined in the wild-type strain
Genome_build: N. punctiforme genome
Supplementary_files_format_and_content: NOT PROVIDED
|
| |
|
| Submission date |
Jul 28, 2021 |
| Last update date |
Jul 31, 2021 |
| Contact name |
Douglas D Risser |
| E-mail(s) |
[email protected]
|
| Phone |
2099322953
|
| Organization name |
University of the Pacific
|
| Department |
Biology
|
| Lab |
Risser
|
| Street address |
3601 Pacific Ave
|
| City |
Stockton |
| State/province |
California |
| ZIP/Postal code |
95211 |
| Country |
USA |
| |
|
| Platform ID |
GPL30445 |
| Series (1) |
| GSE180983 |
Cappable-Seq analysis of the N. punctiforme primary transcriptome during hormogonium development in wild type, and three sigma-factor deletion strains |
|
| Relations |
| BioSample |
SAMN20448041 |
| SRA |
SRX11581466 |
