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| Status |
Public on May 16, 2024 |
| Title |
term-seq_WT_R1 |
| Sample type |
SRA |
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| Source name |
bacteria
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| Organism |
Campylobacter jejuni |
| Characteristics |
strain: NCTC11168
cell type: bacteria
genotype: wildtype
treatment: untreated
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| 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.
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| Extracted molecule |
total RNA |
| Extraction protocol |
total RNA was treated with DNase I to digest genomic DNA and ribosomal RNA was depleted
3’Term protocol: First, the 5’ Illumina sequencing adapter was ligated to the 3’-OH of the RNA molecules and cDNA synthesis was performed using M-MLV reverse transcriptase. Then, first-strand cDNA was fragmented and the 3’ Illumina sequencing adapter was ligated to the 3’ ends of the single-stranded cDNA fragments. Finally, the 3’ cDNA fragments were PCR-amplified, purified with the Agencourt AMPure XP kit (Beckman Coulter Genomics), and analyzed by capillary electrophoresis.
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| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina NextSeq 500 |
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| Data processing |
Demultiplexing using bcl2fastq (Illumina; version: 2.20.0.422)
Reads were quality and adapter trimmed with Cutadapt (versions: 1.17 and 2.5) (Martin, 2011) using a cutoff Phred score of 20 in NextSeq mode.
READemption (version: 0.4.5) (Förstner et al., 2014) was used to align all reads longer than 11 nt to the reference genome of C. jejuni NCTC11168 (NCBI accession number: NC_002163.1; Refseq assembly accession GCF_000009085.1) using segemehl (version: 0.2.0) (Hoffmann et al., 2009) with an accuracy cutoff of 95%.
READemption (version: 0.4.5) (Förstner et al., 2014) was applied to generate two kinds of positional coverage files: default total coverage based on full-length alignments and last base coverage mapping of only the 3’-end base of each alignment. In both cases, sequencing depth-normalized plots were used for visualization in the Integrated Genome Browser (Freese et al., 2016).
Assembly: ASM908v1
Supplementary files format and content: normalized read coverages in wiggle format with full-length alignment based read coverage (*full coverage_forward.wig = plus strand; *full coverage_reverse.wig = minus strand)
Supplementary files format and content: normalized read coverages in wiggle format with last base coverage mapping of only the 3’-end base of each alignment (*last base_forward.wig = plus strand; *last base_reverse.wig = minus strand)
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| Submission date |
Apr 28, 2023 |
| Last update date |
May 16, 2024 |
| Contact name |
Cynthia Sharma |
| Organization name |
University of Würzburg
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| Street address |
Josef-Schneider-Straße 2
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| City |
Würzburg |
| State/province |
Bavaria |
| ZIP/Postal code |
97080 |
| Country |
Germany |
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| Platform ID |
GPL26884 |
| Series (1) |
| GSE230837 |
Investigation of transcript 3' ends in Campylobacter jejuni wildtype and ribonuclease mutants |
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| Relations |
| BioSample |
SAMN34415407 |
| SRA |
SRX20124982 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSM7244867_term-seq_WT_R1_full_coverage_forward.wig.gz |
5.6 Mb |
(ftp)(http) |
WIG |
| GSM7244867_term-seq_WT_R1_full_coverage_reverse.wig.gz |
6.1 Mb |
(ftp)(http) |
WIG |
| GSM7244867_term-seq_WT_R1_last_base_forward.wig.gz |
1.5 Mb |
(ftp)(http) |
WIG |
| GSM7244867_term-seq_WT_R1_last_base_reverse.wig.gz |
1.7 Mb |
(ftp)(http) |
WIG |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data provided as supplementary file |
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