|
| Status |
Public on Dec 06, 2022 |
| Title |
PGM-101: DE442_TEXplus_5prime_dRNA-seq |
| Sample type |
SRA |
| |
|
| Source name |
DE442 TEX+ 5'
|
| Organism |
Rhodobacter capsulatus DE442 |
| Characteristics |
strain: DE442
growth phase: Early Stationary
tissue: whole organism
|
| Growth protocol |
R. capsulatus cells were grown aerobically in RCV minimal medium for one day. Cells were then transferred to an anaerobic photosynthetic tube containing YPS medium. The anaerobic cultures were prepared to have an initial optical density of 20 Klett Units (KU). Cultures were grown for 15-16 hours.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
500μ of culture were transferred into 100μl 95% Ethanol and 5% Phenol. Samples were spun down for 2 minutes and the pellets were stored at -80°C. Small RNA was extracted following the Macherey-Nagel protocol for DNA, RNA, and protein purification kit for small RNA fraction.
Libraries for 5' and 3' targeted sequencing were prepared following a newly developed protocol based on dRNA-seq. Libraries for total RNA seq were prepared following the Ion Torrent Ion Total RNA-Seq Kit V2 for whole RNA Libraries protocol.
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Ion Torrent PGM |
| |
|
| Description |
RNA_2015_09_23_13_04_54
|
| Data processing |
In house software used for data processing
TSSAR software used for detection of transcription start sites and transcription termination sites
In house pipeline used for operon detection
Supplementary_files_format_and_content: allData_transcripts: combined file for each strain containing dRNA-seq 5' and 3' data
Supplementary_files_format_and_content: dRNA_seq_TSSs: correspond to the dRNA-seq 5' data
Supplementary_files_format_and_content: dRNASeq_TTSs: correspond to the dRNA-seq 3' data
|
| |
|
| Submission date |
Jul 23, 2018 |
| Last update date |
Dec 06, 2022 |
| Contact name |
Marc Patrick Grüll |
| E-mail(s) |
[email protected]
|
| Organization name |
Memorial University of Newfoundand
|
| Department |
Biology
|
| Lab |
Andrew S. Lang
|
| Street address |
230 Elizabeth Ave
|
| City |
St John's |
| State/province |
Newfoundland |
| ZIP/Postal code |
A1B 3X9 |
| Country |
Canada |
| |
|
| Platform ID |
GPL25364 |
| Series (1) |
| GSE117537 |
Operon complexity in Rhodobacter capsulatus revealed by integration of dRNA-seq and RNA-seq data |
|
| Relations |
| BioSample |
SAMN09704439 |
| SRA |
SRX4420258 |
