|
| Status |
Public on Jun 20, 2024 |
| Title |
rep3 SVAKO1 EtOH |
| Sample type |
SRA |
| |
|
| Source name |
ATCC 10712
|
| Organism |
Streptomyces venezuelae |
| Characteristics |
cell line: ATCC 10712
cell type: Rmd1
treatment: EtOH
|
| Treatment protocol |
Total RNA was extracted from each sample and used as input material for the sequencing libraries
|
| Growth protocol |
Streptomyces venezuelae strains (WT and mutant derivaties; ATCC 10712) were cultured in both ISP2 media and Glucose-Isoleucine media under standard and stress conditions (6% EtOH or 42oC)
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA was extracted from samples using a Trizol extraction along with bead beating.
MSR-seq (PMID 35513407)
|
| |
|
| Library strategy |
OTHER |
| Library source |
transcriptomic |
| Library selection |
other |
| Instrument model |
Illumina NovaSeq 6000 |
| |
|
| Data processing |
*library strategy: multiplex small RNA sequencing (MSR-seq)
Raw sequences reads were demultiplexed using Je to detect encoded barcode reads. Following this, reads were aligned to curated Streptomyces Venezuelae tRNA and 5s rRNA reference genome.
The aligned reads were then used to determine RNA sequence abundance using custom python script. RNA modifications were detected based on aligned reads using samtools sort (http://www.htslib.org/,Li et al., 2009) feature sort the reads in a bam file format. Then IGVtools count (https://software.broadinstitute.org/software/igv/igvtools) count feature was utilized to output a wig files using the following parameters: -z 5 -w 1 -e 250 —bases. The resulting wig files were processed using a custom python script to identify nucleotide mutations as well as coverage of aligned reads.
Assembly: Streptomyces venezuelae ATCC 10712
Supplementary files format and content: tsv files with gene name and abundance per sample
Supplementary files format and content: .sam.tsv files with mutation, deletion, coverage for each gene position per sample
|
| |
|
| Submission date |
Apr 18, 2024 |
| Last update date |
Jun 20, 2024 |
| Contact name |
Tao Pan |
| E-mail(s) |
taopan@uchicago.edu
|
| Phone |
(773) 702-4179
|
| Organization name |
University of Chicago
|
| Department |
Biochemistry and Molecular Biology
|
| Street address |
929 E. 57th Street
|
| City |
Chicago |
| State/province |
Illinois |
| ZIP/Postal code |
60637 |
| Country |
USA |
| |
|
| Platform ID |
GPL32677 |
| Series (1) |
| GSE264330 |
Prokaryotic N1-methyladenosine erasers maintain tRNA m1A modification levels in Streptomyces venezuelae. |
|
| Relations |
| BioSample |
SAMN41010055 |
| SRA |
SRX24303710 |
