Rep 3: RNAseq from cells grown in MRS-T with 1% DMSO - SRA

Links from BioSample

SRX25387845: Rep 3: RNAseq from cells grown in MRS-T with 1% DMSO
1 ILLUMINA (Illumina NovaSeq 6000) run: 9.5M spots, 2.9G bases, 901.5Mb downloads

Design: Library construction and sequencing was performed by Novogene, (Novogene Co., Davis, CA, USA) . After cluster generation, the library preparations were sequenced on an Illumina platform and paired-end reads were generated. Raw data (raw reads) of FASTQ format were first processed through fastp. The reference genome and gene model annotation files were downloaded from NCBI. Bowtie2 was used to build the index of the reference genome and to align the clean reads. FeatureCounts was used to count the read numbers mapped to each gene. Differential expression analysis was performed using the DESeq2 R package, and the resulting p-values were adjusted using Benjamini and Hochbergs approach for controlling the false discovery rate. Genes with an adjusted p-value < 0.05 found by DESeq were assigned as differentially expressed. Gene Ontology (GO) enrichment analysis of differentially expressed genes was implemented by the clusterProfiler R package, in which gene length bias was corrected. GO terms with a corrected p-value less than 0.05 were considered significantly enriched by differential expressed genes. The clusterProfiler R package was used to test the statistical enrichment of differential expression genes in KEGG pathways.

Submitted by: University of Florida

Study: RNAseq of L.johnsonii N6.2 grown in MRS with erucic acid

PRJNA1137922 • SRP521004 • All experiments • All runs

show Abstracthide Abstract

The goal of this work was to identify changes in gene expression when L. johnsonii N6.2 was cultivated in media containing erucic acid as a sole source of exogenous fatty acids.

Sample: 3

SAMN42644123 • SRS22051676 • All experiments • All runs

Organism: Lactobacillus johnsonii

Library:

Name: DMSO_03

Instrument: Illumina NovaSeq 6000

Strategy: RNA-Seq

Source: TRANSCRIPTOMIC

Selection: RANDOM

Layout: PAIRED

Runs: 1 run, 9.5M spots, 2.9G bases, 901.5Mb

Run	# of Spots	# of Bases	Size	Published
SRR29891847	9,527,091	2.9G	901.5Mb	2024-11-12

ID:: 33861814

SRA

Sequence Read Archive

Result Filters

Send to:

Links from BioSample

Supplemental Content

Related information

Recent activity