|
| Status |
Public on Feb 06, 2014 |
| Title |
Rhodobacter sphaeroides wild type |
| Sample type |
SRA |
| |
|
| Source name |
R_s_WT
|
| Organism |
Cereibacter sphaeroides 2.4.1 |
| Characteristics |
genotype/variation: wild type
|
| Growth protocol |
R. sphaeroides cultures were grown in malate minimal medium (Niel, 1944) at 32°C under micro-aerobic conditions (dissolved oxygen: 25 µM) to an OD660 0.4.
|
| 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 Genome Analyzer IIx |
| |
|
| Description |
R_s_WT
|
| Data processing |
Demultiplexing
FastQ quality trimming using FastX and a cut-off value of 20
Fastq to fasta conversion using FastX
Size filtering: discarding reads shorter than 12 nt (TRAPL)
Read mapping using segemehl version 0.1.4 (TRAPL)
Coverage calculation and normalization (TRAPL)
Genome_build: ASM1290v1 [CP000143.1, CP000144.1, CP000145.1, CP000146.1, CP000147.1, DQ232586.1, DQ232587.1]
Supplementary_files_format_and_content: [wiggle file] Normalized (by total number of aligned reads) read coverages multiplied by 1M in wiggle format (*_forward.wig = forward strand; *_minus.wig= forward strand)
|
| |
|
| Submission date |
Feb 06, 2014 |
| 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 |
GPL18261 |
| Series (1) |
| GSE54750 |
RNase J is required for processing of a small number of RNAs in Rhodobacter sphaeroides |
|
| Relations |
| BioSample |
SAMN02630183 |
| SRA |
SRX466453 |
