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| Status |
Public on Feb 20, 2024 |
| Title |
MG1655 30min -2 |
| Sample type |
SRA |
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| Source name |
MG1655
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| Organism |
Escherichia coli |
| Characteristics |
strain: MG1655
genotype: K-12 F-lambda-
cell type: bacterial cell
treatment 1: L-arabinose (0,2%)
treatment 2: /
time: 30 min
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| Treatment protocol |
tisB was induced with L-arabinose (0.2%) for 30 min.
L-arabinose was removed by washing with 0.9% NaCl and cells were resuspended in LB medium for recovery.
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| Growth protocol |
Cells were grown in LB medium at 37°C and shaking at 180 rpm.
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| Extracted molecule |
total RNA |
| Extraction protocol |
RNA was isolated according to the hot acid-penol method. DNA was removed with TURBO DNA-freeTM kit (Invitrogen) according to "rigorous treatment" instructions. The final clean-up was performed using phenol/chloroform/isoamyl alcohol (25:24:1) mixed with the sample in a 1:1 ratio, followed by chloroform treatment and precipitation.
For cDNA synthesis, all RNA samples were first fragmented using ultrasound (4 pulses of 30 seconds, each at 4°C). Then, an oligonucleotide adapter was ligated to the 3’ end of the RNA molecules. First-strand cDNA synthesis was performed using M-MLV reverse transcriptase and the 3’ adapter as primer. The first-strand cDNA was purified and the 5’ Illumina TruSeq sequencing adapter was ligated to the 3’ end of the antisense cDNA. The resulting cDNA was PCR-amplified to about 10-20 ng/µl using a high-fidelity DNA polymerase for 12 cycles. The TruSeq barcode sequences, which are part of the 5’ and 3’ TruSeq sequencing adapters, were used. The cDNA was purified using 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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| Description |
X0ATG.2_S5_R1_001
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| Data processing |
Quality and adapter trimming was performed with Trim Galore (Version 0.6.5) with Cutadapt Version 2.7 using the parameters ‘--quality 20 --length 20’ and default adapter detection and trimming.
MultiQC (Version 1.8) and FastQC (Version 0.11.8) were used for quality control.
The preprocessed reads were aligned with Bowtie2 (Version 2.3.5) using the ‘--mm’ and ‘--very-sensitive’ settings and GCF_000005845.2 (NCBI; downloaded 25.11.2019) as a reference genome.
For postprocessing of the alignments, gene counting and data analysis, Samtools (Version 1.9), featureCounts (Version 1.6.4) and DESeq2 (Version 1.26) were applied, respectively.
All bioinformatic calculations were performed using Curare (Version 0.1.1) and R statistical language.
Assembly: GCF_000005845.2
Supplementary files format and content: Excel file containing normalized read counts of each sample and DESeq2 comparison between conditions.
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| Submission date |
Feb 14, 2024 |
| Last update date |
Feb 20, 2024 |
| Contact name |
Bork A. Berghoff |
| Organization name |
University of Giessen
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| Street address |
Heinrich-Buff-Ring 26-32
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| City |
Giessen |
| ZIP/Postal code |
35392 |
| Country |
Germany |
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| Platform ID |
GPL21222 |
| Series (1) |
| GSE255764 |
Analysis of the stress response after induction of the dormancy-inducing membrane toxin TisB in Escherichia coli |
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| Relations |
| BioSample |
SAMN39942936 |
| SRA |
SRX23620290 |
| Supplementary data files not provided |
SRA Run Selector |
| Raw data are available in SRA |
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