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Sample GSM7785077

Query DataSets for GSM7785077

Status

Public on Sep 19, 2023

Title

Helicobacter pylori, CagA KO, rep1

Sample type

SRA

Source name

Helicobacter pylori

Organism

Helicobacter pylori

Characteristics

cell type: Helicobacter pylori
hp genotype: CagA KO

Growth protocol

Helicobacter pylori were maintained in columbia blood agar medium at 37℃.GES-1 cells were maintained in 1640 supplemented with 10% fetal bovine serum(FBS) in humidified atmosphere with 5% CO2 at 37℃.

Extracted molecule

total RNA

Extraction protocol

Total RNA was extracted using Trizol reagent kit (Invitrogen, Carlsbad, CA,USA) according to the manufacturer’s protocol.
After total RNA was extracted, eukaryotic mRNA was enriched by Oligo(dT)beads(Pronucleus：After total RNA was extracted, prokaryotic mRNA was enriched by removing rRNA by Ribo-ZeroTM Magnetic Kit (Epicentre, Madison, WI, USA)). Then the enriched mRNA was fragmented into short fragments using fragmentation buffer and reversly transcribed into cDNA by using NEBNext Ultra RNA Library Prep Kit for Illumina(NEB#7530,New England Biolabs, Ipswich, MA, USA)

Library strategy

RNA-Seq

Library source

transcriptomic

Library selection

cDNA

Instrument model

Illumina NovaSeq 6000

Description

KO-1

Data processing

www.genedenovo.com
Reads were filtered by fastp (version 0.18.0).The parameters were as follows: 1) removing reads containing adapters; 2) removing reads containing more than 10% of unknown nucleotides(N); 3) removing low quality reads containing more than 50% of low quality (Q-value≤20) bases.
Short reads alignment tool Bowtie2 (version 2.2.8) was used for mapping reads to ribosome RNA (rRNA) database.The rRNA mapped reads then will be removed. The remaining clean reads were further used in assembly and gene abundance calculation.
An index of the reference genome was built, and paired-end clean reads were mapped to the reference genome using HISAT2. 2.4 and other parameters set as a default.
The mapped reads of each sample were assembled by using StringTie v1.3.1 in a reference-based approach.
Supplementary files format and content: tab-delimited text file includes raw counts for each sample.
Supplementary files format and content: tab-delimited text file includes FPKM values for each sample.

Submission date

Sep 18, 2023

Last update date

Sep 19, 2023

Contact name

Zhiyong Zhai

E-mail(s)

drzzy0930@outlook.com

Phone

+8615626446461

Organization name

Shenzhen Hospital of Southern Medical University