|
| Status |
Public on Aug 22, 2023 |
| Title |
BW25113 csdA KO, ADRPC-, rep1 |
| Sample type |
SRA |
| |
|
| Source name |
csdA KO in the E. coli K-12 background strain BW25113
|
| Organism |
Escherichia coli |
| Characteristics |
strain: csdA KO in the E. coli K-12 background strain BW25113
genotype: F-, {delta}(araD-araB)567, {delta}lacZ4787(::rrnB-3),{lambda}-, {delta}csdA738::kan, rph-1, {delta}(rhaD-rhaB)568, 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.
NAD captureSeq libraries were prepared according to the modified protocol provided by (Winz et al. 2017).
|
| |
|
| 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 trimmed with SeqPurge and cutadapt.
Processed reads were mapped to the reference Escherichia coli BW25113 strain K-12 (NZ_CP009273.1) genome using hisat2 v2.2.0 (options --score-min L,0,-0.3 --no-unal --no-mixed —no-spliced-alignment).
5’-NAD-RNA were identified using DESeq2 package (quantification performed with stringtie)
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) |
| GSE224605 |
5’-NAD-RNA identification in E. coli BW25113 wt, nudC and csdA knockouts |
| GSE224608 |
Interplay between bacterial RNA 5'-termini deNADding protein NudC and DEAD-box RNA helicase CsdA in stress-responses |
|
| Relations |
| BioSample |
SAMN33138956 |
| SRA |
SRX19290098 |
