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RNA sequencing of vtRNA-knockout HEK293T cell lines

GSE335700 Homo sapiens (human) RNA-seq (gene expression) 36 samples Submitted 2026/06/17 Platform GPL34284
At a glance

RNA-seq (gene expression) · human · 36 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
36 samples: 12 conditions, mostly in triplicateGroups 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)
HEK293T cell lines lacking one or more of the human VTRNA1 paralogs, alongside wild-type parental cells, had their RNA sequenced by Plasmidsaurus (poly-A enrichment) and/or Genewiz (rRNA depletion). Differential expression was performed to determine transcriptomic effects of vtRNA knockout, as well as to compare the two sequencing approaches.
This dataset
Open GSE335700 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 GSE335700_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 PRJNA1479262 and SRA study SRP710310. Searching any of these in the dataset finder brings you back here.

NCBI GEO page ↗
Study design
12 conditions, mostly in triplicate
Plasmidsaurus seq, wild-type, ×3 Plasmidsaurus seq, vtRNA1-1 knockout, ×3 Plasmidsaurus seq, vtRNA1-2 knockout, ×3 Plasmidsaurus seq, vtRNA1-3 knockout, ×3 Plasmidsaurus seq, vtRNA1 triple-knockout, cl… ×3 Plasmidsaurus seq, vtRNA1 triple-knockout, cl… ×3 Plasmidsaurus seq, vtRNA1 triple-knockout, cl… ×3 Plasmidsaurus seq, control deletion, ×3 +4 more

Supports a case/control comparison: 27 samples read as cases, 9 as controls.

How we read this: 12 replicated groups read from 36 sample titles; they account for 36 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
Datasets on a similar topic

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