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Sample GSM8307187

Query DataSets for GSM8307187

Status

Public on Jun 10, 2024

Title

sp replicate3

Sample type

SRA

Source name

bacteria

Organism

Salmonella enterica subsp. enterica serovar Pullorum

Characteristics

cell type: bacteria
genotype: WT
treatment: standard strain

Extracted molecule

total RNA

Extraction protocol

1 µg of total RNA was treated sequentially with phosphatase and PNK kinase (New England Biolabs). The treated RNA was subjected to library construction by GenSeq's Small RNA Library Kit. The QC-controlled libraries were subjected to 150bp bipartite sequencing by Illumina NovaSeq High-Throughput Sequencer.
RNA libraries were prepared for sequencing using standard Illumina protocols

Library strategy

ncRNA-Seq

Library source

transcriptomic

Library selection

size fractionation

Instrument model

Illumina NovaSeq 6000

Data processing

1 μg total RNA was firstly treated with Antarctic phosphatase (New England Biolabs) and then with PNK enzyme (New England Biolabs). RNA Library was prepared with treated RNA according to the manufacturer’s instructions of GenSeq® Small RNA Library Prep Kit (GenSeq Inc.). The libraries were size-selected for sRNA fraction (50–500 nt) with TBE polyacrylamide gel. Libraries were controlled for quality and quantified using the BioAnalyzer 2100 system (Agilent Technologies, Inc., USA). The libraries were sequenced for 150 pair-end cycles on Illumina NovaSeq Sequencer according to the manufacturer’s instructions (Illumina, San Diego, USA).
Paired-end reads were harvested from Illumina NovaSeq 6000 sequencer, and were quality controlled by Q30.After 3’ adaptor-trimming and low quality reads removing by cutadapt software (v1.9.3).
sRNA candidates are predicted using sRNAscanner based on transcriptional signals. sRNA overlapping with known genes are excluded and the rest are added into the gene annotation of the genome.
The clean reads were aligned to the reference genome using Hisat2 software. HTSeq was used to count the read numbers mapped to each gene. edgeR was used to normalizing the read counts for each library and to identifying differentially expressed genes.
Assembly: ASM360622v1
Supplementary files format and content: The processed data is in xlsx format and contains sRNA reads, location and length, etc.

Submission date

Jun 05, 2024

Last update date

Jun 10, 2024

Contact name

HE Ting

E-mail(s)

ht1723595275@outlook.com

Phone

15708925598

Organization name

Hainan University