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Transcriptomic analysis of Hsp90 inhibitor (Hsp90i)-treated HIV-infected pediatric tonsillar mononuclear cells

GSE178178 Homo sapiens (human) RNA-seq (gene expression) 16 samples Submitted 2024/06/14 Platform GPL20301
At a glance

RNA-seq (gene expression) · human · 16 samples

What it is
RNA-seq (gene expression)Gene activity measured by sequencing. The summary does not mention single-cell work, so this is most likely bulk: one average per sample, the usual starting point for comparing groups.
Organism
Homo sapiens (human)
Samples
16 samples: 16 samples, each with a distinct title — no replicated groupsGroups are read from the sample names, not from the paper. Check the list below.
Data you can get
A processed table (series matrix) and supplementary files from NCBI; the raw sequencing reads from ENA. Which of these hold counts depends on the study, so check the file list.
Summary (written by the submitters)
Purpose: Hsp90 is a host chaperone protein that regulates cellular homeostasis by interacting with a diverse clientele of cellular proteins. Several of these proteins are involved in cellular pathways that play crucial roles in facilitating HIV replication. Identification of key cellular genes that are utilized by HIV for their replication, and whose expression is altered by Hsp90i, will lead to the development of targeted HIV therapeutics, which will ultimately be utilized for HIV cure.
Read the full summary ↓
Here we characterized the key cellular genes altered upon Hsp90i treatment of HIV-infected pediatric tonsillar mononuclear cells. Methods: Discarded tonsil tissues from 8 independent donors <15 years of age were obtained through Duke University School of Medicine Biorepository and Precision Pathology Center (BRPC), during routine tonsillectomy. Tonsil tissues were washed and minced in RPMI 1640 (Gibco), containing 1X antibiotic/antimycotic mixture (Gibco), 50μg/ml Gentamicin (Gibco), 10μg/ml Cephalothin (Sigma-Aldrich) and 5μg/ml Fluconazole (Sigma-Aldrich), and tonsillar mononuclear cells (TMCs) were isolated by filtering tonsillar tissue pieces through a 70-μm mesh filter, followed by density gradient centrifugation using Ficoll-Paque PLUS (GE Healthcare, Waukesha, WI). 5x105 TMCs were infected with 250ng p24 equivalent of the cell-free CCR5-tropic HIV-JRFL virus. After 24hr, virus- infected cells were treated with either 0.1% DMSO or 0.1μM Hsp90i, daily. After 96hrs, total cellular RNA was extracted from TMCs using RNAeasy Mini kit (Qiagen). Total RNA quality and quantity was assessed using the Agilent Bionalyzer 2100 and the Qubit fluorometer, respectively. Poly(A) mRNA capture and construction of stranded mRNA-seq libraries from intact total RNA (RIN >7) was achieved using the commercially available KAPA Stranded mRNA-Seq Kit. In brief, mRNA transcripts were first captured from 200ng of total RNA using magnetic oligo-dT beads, fragmented using heat and magnesium, and reverse transcribed to produce dscDNA. Illumina sequencing adapters were then ligated to the dscDNA fragments and amplified to produce the final RNA-seq library. Libraries were indexed using dual molecular indices allowing for multiple libraries to be pooled and sequenced on the same sequencing lane on a HiSeq 4000 Illumina sequencing platform. Before pooling and sequencing, fragment length distribution and library quality was assessed on a 2100 Bioanalyzer using the High Sensitivity DNA Kit (Agilent Technologies). All libraries were then pooled in equimolar ratio and sequenced. Multiplexing 8 libraries on one lane of an Illumina HiSeq 4000 flow cell yielded about 43 million 50bp sequences per sample. Once generated, sequence data was de-multiplexed and Fastq files generated using Bcl2Fastq conversion software provided by Illumina. Conclusion: This study identified differentially expressed genes between DMSO-treated and Hsp90i-treated HIV-infected pediatric tonsillar mononuclear cells.
This dataset
Open GSE178178 in finder → Find more human RNA-seq datasets →
Download · which file do I need?

Direct links to NCBI and ENA, no account and no request form. Pick by what you want to do: take the small processed table to look, the supplementary files to re-analyse, or the original raw data to start over.

1 · Just have a look

Processed table

The series matrix: one table of values per sample as the submitters processed it. The smallest download, and it opens in Excel or R. Start here to see what the data look like.

Series matrix ↓
2 · Re-analyse it

Supplementary files

The count tables and other files the authors uploaded. Take only the samples you need, or the whole study as GSE178178_RAW.tar (it can run to tens of gigabytes).

All supplementary files ↗ Whole study · RAW.tar ↓
3 · Start from the raw reads

Raw sequencing reads

The original FASTQ files, straight from the sequencer, held at ENA. Large, and you align them yourself, so only choose this if you need to re-process the study from scratch.

Raw reads on ENA ↗

What the files usually look like: For RNA-seq the counts are usually a table among the supplementary files (look for 'counts', 'expression', 'FPKM' or 'TPM' in the file name). The series matrix of a sequencing study is sometimes nearly empty.

Also filed as BioProject PRJNA737514 and SRA study SRP324034. Searching any of these in the dataset finder brings you back here.

NCBI GEO page ↗
Study design
16 samples, each with a distinct title — no replicated groups

Any grouping that defines a comparison lives in the sample characteristics, which GEO records separately from the titles.

How we read this: Read from 16 sample titles: 16 distinct titles with little repetition. These groups are guessed from the sample names, not taken from the paper, so check them against the sample list below before relying on them.

Samples in this study
Datasets on a similar topic

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