 |
 |
GEO help: Mouse over screen elements for information. |
|
| Status |
Public on May 16, 2024 |
| Title |
dRNA-seq_WT_-TEX_R1 |
| Sample type |
SRA |
| |
|
| Source name |
bacteria
|
| Organism |
Campylobacter jejuni |
| Characteristics |
strain: NCTC11168
cell type: bacteria
genotype: wildtype
treatment: untreated
|
| Growth protocol |
Bacteria were grown in Brucella Broth (supplemented with 10 µg/ml vancomycin) at 37°C in a microaerobic atmosphere (10% CO2, 5% O2) until log phase.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
total RNA was treated with DNase I to digest genomic DNA, terminator exonuclease treatment of one half of each RNA sample
small RNA protocol, as previously described (Berezikov et al., 2006), but without RNA fractionation prior to cDNA synthesis: Equal amounts of RNA were poly(A)‐tailed using poly(A) polymerase and 5’-triphosphate groups were digested with tobacco acid pyrophosphatase (TAP). Then, an RNA adapter was ligated to the 5’ phosphate and first‑strand cDNA synthesised with an oligo(dT)‐adapter primer and M‑MLV (Moloney Murine Leukaemia Virus) reverse transcriptase. A high-fidelity DNA polymerase was used to PCR‐amplify the resulting cDNA to a concentration of ~20‐30 ng/μl. Finally, cDNA was purified with the Agencourt AMPure XP kit (Beckman Coulter Genomics) and analyzed by capillary electrophoresis.
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 2000 |
| |
|
| Data processing |
Demultiplexing
FASTQ-format reads were trimmed with a cutoff Phred score of 20 using Cutadapt (version: 4.1) (Martin, 2011).
After poly(A)‐tails were removed, sequences shorter than 12 nt were omitted and the remaining reads mapped to the C. jejuni NCTC11168 reference genome (NCBI accession number: NC_002163.1, RefSeq assembly accession number: GCF_000009085.1) using READemption (version: 2.0.1) (Förstner et al., 2014) and segemehl (version: 0.3.4) (Hoffmann et al., 2009) with an accuracy cutoff of 95%.
Coverage plots containing the number of mapped reads per nucleotide were also generated with READemption and visualized in the Integrated Genome Browser (Freese et al., 2016). The coverage was normalized by the total number of aligned reads of a given library and multiplied by the minimum number of aligned reads calculated over all libraries.
Assembly: ASM908v1
Supplementary files format and content: normalized read coverages in wiggle format with full-length alignment based read coverage (*_forward.wig = plus strand; *_reverse.wig = minus strand)
|
| |
|
| Submission date |
Apr 28, 2023 |
| Last update date |
May 16, 2024 |
| Contact name |
Cynthia Sharma |
| Organization name |
University of Würzburg
|
| Street address |
Josef-Schneider-Straße 2
|
| City |
Würzburg |
| State/province |
Bavaria |
| ZIP/Postal code |
97080 |
| Country |
Germany |
| |
|
| Platform ID |
GPL17549 |
| Series (1) |
| GSE230836 |
Investigation of RNA 5' ends in Campylobacter jejuni wildtype and an RNase III mutant strain |
|
| Relations |
| BioSample |
SAMN34415354 |
| SRA |
SRX20124979 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSM7244864_dRNA-seq_WT_-TEX_R1_forward.wig.gz |
3.9 Mb |
(ftp)(http) |
WIG |
| GSM7244864_dRNA-seq_WT_-TEX_R1_reverse.wig.gz |
4.1 Mb |
(ftp)(http) |
WIG |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data provided as supplementary file |
|
|
|
|
 |
