|
| Status |
Public on Aug 22, 2023 |
| Title |
BW25113 nudC KO, replicate 2 |
| Sample type |
SRA |
| |
|
| Source name |
nudC KO in the E. coli K-12 background strain BW25113
|
| Organism |
Escherichia coli |
| Characteristics |
strain: nudC KO in the E. coli K-12 background strain BW25113
genotype: F-, {delta}(araD-araB)567, {delta}lacZ4787(::rrnB-3),{lambda}-, rph-1, {delta}(rhaD-rhaB)568, {delta}nudC767::kan, hsdR514
|
| Growth protocol |
Bacteria cultures were grown in LB medium at 24°C till exponential growth phase and collected after premixing with 1/8 volume of ice-cold STOP solution (5% acid phenol, 95% ethanol).
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA was extracted using RNazol RT (RN 190) (Molecular Research Center, Inc.) according to the manufacturer’s recommendations.
rRNAs were depleted using RiboMinus Bacteria 2.0 Transcriptome Isolation Kit (Invitrogen). The remaining RNA was fragmented into approximately 100-400 nt long pieces in ZnCl2 buffer and dephosphorylated using T4 PNK (Thermo Fisher Scientific). 140 ng of fragmented and dephosphorylated RNA was then used for RNA library preparation according to the NEXTflex Small RNA-seq Kit v3 (PerkinElmer) with minor modifications: at Steps E and G incubation at 42°C and 72°C was extended to 60 min, at Step G 9 PCR cycles were performed and Steps F and H1 were carried out as described in an alternative protocol for Preparing Libraries without Size Selection. RNA libraries up to 500 nt in length were purified from PAA gel as outlined in Step H2.
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
NextSeq 2000 |
| |
|
| Data processing |
The quality of raw sequencing reads was evaluated using FASTQC program v0.11.9. Reads were quality (PHRED threshold 20) and length (minimum length 20) filtered using Trim Galore! v0.6.5
Processed reads were mapped to the reference Escherichia coli BW25113 strain K-12 (NZ_CP009273.1) genome using hisat2 v2.2.0 (options —no-unal --no-spliced-alignment -X 500 --no-mixed —no-discordant) and deduplicated using UMI-tools.
Gene expression was evaluated using StringTie using NCBI gene annotation (sRNAs were added manually). Differentially expressed genes were identified using DESeq2 package.
Assembly: NZ_CP009273.1
Supplementary files format and content: tab-delimited text files include transcripts coordinates, coverage and FPKM values for each Sample
|
| |
|
| Submission date |
Feb 06, 2023 |
| Last update date |
Aug 22, 2023 |
| Contact name |
Kotryna Kvederaviciute |
| E-mail(s) |
kotryna.kvederaviciute@mif.vu.lt
|
| Organization name |
Vilnius University
|
| Department |
Life Sciences Center
|
| Lab |
Institute Of Biotechnology
|
| Street address |
Sauletekio av. 7
|
| City |
Vilnius |
| ZIP/Postal code |
10257 |
| Country |
Lithuania |
| |
|
| Platform ID |
GPL32081 |
| Series (2) |
| GSE224606 |
Whole transcriptome sequencing of E. coli BW25113 wt and nudC knockout strains |
| GSE224608 |
Interplay between bacterial RNA 5'-termini deNADding protein NudC and DEAD-box RNA helicase CsdA in stress-responses |
|
| Relations |
| BioSample |
SAMN33138911 |
| SRA |
SRX19290083 |
