NCBI Logo
GEO Logo
   NCBI > GEO > Accession DisplayHelp Not logged in | LoginHelp
GEO help: Mouse over screen elements for information.
          Go
Sample GSM7027238 Query DataSets for GSM7027238
Status Public on Aug 22, 2023
Title BW25113 wt, replicate 2
Sample type SRA
 
Source name E. coli K-12 background strain BW25113
Organism Escherichia coli
Characteristics strain: E. coli K-12 background strain BW25113
genotype: F-, {delta}(araD-araB)567, {delta}lacZ4787(::rrnB-3),{lambda}-, 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.
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 SAMN33138914
SRA SRX19290080

Supplementary file Size Download File type/resource
GSM7027238_wt_rep2.tsv.gz 138.7 Kb (ftp)(http) TSV
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file

| NLM | NIH | GEO Help | Disclaimer | Accessibility |
NCBI Home NCBI Search NCBI SiteMap