|
| Status |
Public on Mar 08, 2017 |
| Title |
R_s_stationary_phase_TEX_pos |
| Sample type |
SRA |
| |
|
| Source name |
bacterial cells
|
| Organism |
Cereibacter sphaeroides 2.4.1 |
| Characteristics |
phase: stationary
treatment: with TEX (terminator exonuclease treatment)
|
| Growth protocol |
Rhodobacter sphaeroides was grown in low aeration (25-30 µM oxygen)
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA was isolated using the hot phenol method followed by two chloroform-isoamyl alcohol treatments and precipitation with sodium acetate and ethanol. RNA was resolved in RNase free water (Roth) and concentrations were determined at a NanoDrop 1000 Spectrophotometer (Peqlab). The sample was treated with DNaseI (Invitrogen) to remove DNA.
The libraries were generated by Vertis Biotechnologie AG (Munich, Germany). The samples were poly(A)-tailed by using poly(A) polymerase. The 5'-PPP were removed using tobacco acid pyrophosphatase (TAP) followed by the ligation of the RNA adapter to the 5'-monophosphate of the RNA. First-strand cDNA synthesis was performed with an oligo(dT)-adapter primer and the M-MLV reverse transcriptase. The resulting cDNA was PCR-amplified to reach a concentration of 20-30 ng/μl using a high fidelity DNA polymerase. The cDNA was purified using the Agencourt AMPure XP kit (Beckman Coulter Genomics) and was analyzed by capillary electrophoresis. The primers used for PCR amplification were designed for TruSeq sequencing according to the instructions of Illumina
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 2000 |
| |
|
| Data processing |
FastQ quality trimming using FastX (version 0.0.13) and a cut-off value of 20
Fastq to fasta conversion using FastX FastX (version 0.0.13)
Size filtering: discarding reads shorter than 20 nt (READemption version 0.3.5)
Read mapping using segemehl version 0.2.0 (READemption version 0.3.5)
Coverage calculation and normalisation (READemption version 0.3.5)
Genome_build: NC_007488.2, NC_007489.1, NC_007490.2, NC_007493.2, NC_007494.2, NC_009007.1, NC_009008.1
Supplementary_files_format_and_content: wig
|
| |
|
| Submission date |
Aug 07, 2015 |
| Last update date |
May 15, 2019 |
| Contact name |
Konrad U. Förstner |
| E-mail(s) |
foerstner@zbmed.de
|
| Organization name |
ZB MED - Information Centre for Life Sciences
|
| Department |
Information Services
|
| Lab |
Förstner Lab
|
| Street address |
Gleueler Str. 60
|
| City |
Cologne |
| State/province |
North Rhine-Westphalia |
| ZIP/Postal code |
50931 |
| Country |
Germany |
| |
|
| Platform ID |
GPL17213 |
| Series (1) |
| GSE71844 |
Growth-phase dependent gene regulation in the alpha-proteobacterium Rhodobacter sphaeroides |
|
| Relations |
| SRA |
SRX1136772 |
| BioSample |
SAMN03979888 |
