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Comprehensive mRNA-sequencing-based characterization of three HEK-293 cell lines during an rAAV production process for Gene Therapy Applications

GSE226054 Homo sapiens (human) RNA-seq (gene expression) 120 samples Submitted 2024/05/13 Platform GPL24676
At a glance

RNA-seq (gene expression) · human · 120 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
120 samples: 24 conditions, mostly with about 5 replicates eachGroups 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.
Paper
Enhancement of rAAV titers via inhibition of the interferon signaling cascade in transfected HEK293 suspension culturesBiotechnology journal · 2024
Summary (written by the submitters)
Human embryonal kidney cells (HEK-293) are the most common host cells used for transient recombinant adeno-associated virus (rAAV) production in pharmaceutical industry. To better cover the expected gene therapy product demands in the future, different traditional strategies such as cell line sub-cloning and/or addition of chemical substances to the fermentation media have been used to maximize titers and improve product quality.
Read the full summary ↓
A more effective and advanced approach to boost yield can be envisaged by characterizing the transcriptome of different HEK-293 cell line pedigrees with distinct rAAV productivity patterns to subsequently identify potential gene targets for cell engineering. In this work, the mRNA expression profile of three HEK-293 cell lines, resulting in various yields during a fermentation batch process for rAAV production, was investigated to gain basic insight into cell variability and eventually to identify genes that correlate with productivity. Mock runs using only transfection reagents were performed in parallel as a control. We found significant differences in gene regulatory behaviors between the three cell lines at different growth and production stages. The evaluation of these transcriptomics profiles combined with collected in-process control parameters and titers shed some light on potential cell engineering targets to maximize transient production of rAAV in HEK-293 cells Comparison of three HEK-293 suspension cell lines transcriptomics during an AAV production process
Published in
Enhancement of rAAV titers via inhibition of the interferon signaling cascade in transfected HEK293 suspension cultures
Kahlig CI, Moser S, Micutkova L et al. · Biotechnology journal 2024 · PMID 38719621 · doi:10.1002/biot.202300672
This dataset
Open GSE226054 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 GSE226054_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 PRJNA938438 and SRA study SRP424429. Searching any of these in the dataset finder brings you back here.

NCBI GEO page ↗ Paper (PMID 38719621) ↗
Study design
24 conditions, mostly with about 5 replicates each
C_1T ×5 C_2T ×5 C_3T ×5 C_4T ×5 C_5M ×5 C_6M ×5 C_7M ×5 C_8M ×5 +16 more

Supports a between-group comparison across 120 samples.

How we read this: 24 replicated groups read from 120 sample titles; they account for 120 of them. 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

+ 80 more — browse all 120 samples with per-sample file links →

Datasets on a similar topic

Search all human RNA-seq datasets in GEO →

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