Project description:We recovered RNA from exponential and stationary phase cell cultures of MGAS2221 and utilized two distinct methods to remove rRNA from our samples, the RiboZero kit from Epicenter, and the terminator- 5--Phosphate-Dependent Exonuclease (TEX). This gave us 4 distinct RNAs with which we performed RNAseq analysis. Both rRNA removal methods worked well, with only a small percentage of the final total read counts being derived from rRNA sequences.

2013-03-20 | GSE45325 | GEO

Hypoxic transcriptomic signature of A549 cells (RNA-Seq)

Project description:To assess the transcriptomic response of the LUAD cell line A549 to hypoxia, cells were exposed to 1% (Hx) or 21% O2 (Nx) during 24 hours. Two µg of total RNAs were depleted from ribosomal RNA with the Ribozero kit (epicenter), libraries were generated with the NEBNext Small RNA Library Prep Set for SOLiD and sequenced on SOLiD 5500XL (Life Technologies) with single-end 50bp reads. Reads were aligned to the human genome release hg19 with the LifeScope software v2.5.1 (Life Technologies) using whole transcriptome pipeline for RNA‐seq libraries with default parameters.

2019-09-04 | GSE117048 | GEO

Covid19 RNAseq BAM files

Project description:RNA Sequencing using IlluminaÃ¢Â€Â™s TruSeq Stranded Total RNA with RiboZero Globin depletion library pre kit and sequencing on the NovaSeq 6000.

| EGAS00001007050 | EGA

Covid19 RNAseq Fastq files

Project description:RNA Sequencing using IlluminaÃ¢Â€Â™s TruSeq Stranded Total RNA with RiboZero Globin depletion library pre kit and sequencing on the NovaSeq 6000.

| EGAS00001007022 | EGA

Transcriptomic exploration of SSR42 and its impact on Staphylococcus aureus virulence

Project description:Perhaps the most pivotal feature contributing to Staphylococcus aureus pathogenicity is the production of a wealth of virulence factors such as secreted toxins, adhesive proteins, and factors that aid in host immune evasion. The abundance and activity of these factors is tightly regulated by a multitude of effectors, including two-component systems, alternative sigma factors, DNA binding transcription factors, and regulatory RNAs. SSR42 is a ~1,200-nt long regulatory RNA that has been previously shown to be highly stable and abundant in stationary phase growth. To explore the role of SSR42 within the S. aureus cell, we created a full deletion mutant for this gene and performed RNA sequencing analysis after 15h of growth. Following standardized bacterial growth and sample processing, total bacterial RNA was isolated utilizing the Qiagen RNeasy mini kit and contaminating DNA was removed by treatment with Ambion DNA-free kit. Total RNA was enriched for mRNA using MicrobExpress kit and Illumina RiboZero rRNA removal kit for Gram-positive bacteria. Library construction was performed using the TruSeq Stranded mRNA Kit from Illumina, and RNA was sequenced using an Illumina Nextseq 550. When compared to wild-type, the SSR42 mutant exhibited profound changes in its transcriptomic landscape, suggesting that SSR42 has myriad regulatory targets across niches of function.

2023-07-25 | GSE237701 | GEO

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