2025-06-01
ENA first public
ERC000011
ENA-CHECKLIST
The Racah Institute of Physics The Hebrew University of Jerusalem Jerusalem 9112001, Israel
INSDC center name
public
INSDC status
ERS18601450
SRA accession
E-MTAB-13941:Sample 18
Submitter Id
ArrayExpress
broker name
not collected
collection date
Protocols: Microcolonies were selected from urine of a patient with a UTI infection on LB plate are kept at -80C. Bacteria were regrown in LB at 37C with shaking for 5h. DNA was extracted from 1 mL of bacteria using the DNeasy Blood & Tissue Kit (Qiagen).  Library preparation and sequencing was carried out by BGI company, China. Concentration of samples was detected by fluorometer or Microplate Reader (Qubit Fluorometer, Invitrogen). Sample integrity and purity were detected by Agarose Gel Electrophoresis (Concentration of Agarose Gel:1% Voltage:150 V, Electrophoresis Time:40 min). 1μg genomic DNA was randomly fragmented by Covaris. The fragmented genomic DNA were selected by Agencourt AMPure XP-Medium kit to an average size of 200-400bp. Fragments were end repaired and then 3’ adenylated. Adaptors were ligated to the ends of these 3’ adenylated fragments. PCR products were purified by the Agencourt AMPure XP-Medium kit. The double stranded PCR products were heat denatured and circularized by the splint oligo sequence. The single strand circle DNA (ssCir DNA) were formatted as the final library. Samples were deep-sequenced with the DNBseq G400 machine using the 150-cycles paired-end with 350 bp insert size. At least 150X sequencing depth for each nucleotide in each sample was targeted.
description
not collected
geographic location (country and/or sea)
microcolony bacterial culture from UTI patient
growth condition
not applicable
isolate
mixed sample
organism
mixed sample
organism
whole organism
organism part
mixed sample
scientific_name
UTI_27
strain
Sample 18
title