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RamDA-seq analysis of CRISPRa-mediated RELA activation for proof-of-concept validation of CATaN

GSE335951 Homo sapiens (human) RNA-seq (gene expression) 36 samples Submitted 2026/06/29 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: 18 conditions, mostly in duplicateGroups 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)
This dataset was generated to validate CATaN (Canonical correlation Analysis of Transcriptome and TF-gene regulatory Networks), an unsupervised framework that integrates transcriptomic data with transcription factor (TF) gene regulatory networks. To test whether CATaN correctly recovers the transcriptional program driven by a specific TF, we activated RELA, a subunit of NF-κB, in Jurkat cells using CRISPR activation (CRISPRa; dCas9-VP64 with a single guide RNA targeting RELA) and compared it with a control guide RNA.
Read the full summary ↓
Transcriptomes were profiled by RamDA-seq. Transductions were performed in triplicate for each condition, and cells were harvested at five, six, and seven days post-transduction. Differential expression analysis showed concordant directional changes in RELA-regulated genes; CATaN applied to these data assigned higher CC1 loadings to RELA ChIP-seq samples than to other TFs. Together, these results provide proof-of-concept support for the method.
This dataset
Open GSE335951 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 GSE335951_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 PRJNA1479995 and SRA study SRP710912. Searching any of these in the dataset finder brings you back here.

NCBI GEO page ↗
Study design
18 conditions, mostly in duplicate
Jurkat cells, sgControl, Day 5, biol rep 1, l… ×2 Jurkat cells, sgControl, Day 5, biol rep 2, l… ×2 Jurkat cells, sgControl, Day 5, biol rep 3, l… ×2 Jurkat cells, sgRELA, Day 5, biol rep 1, libr… ×2 Jurkat cells, sgRELA, Day 5, biol rep 2, libr… ×2 Jurkat cells, sgRELA, Day 5, biol rep 3, libr… ×2 Jurkat cells, sgControl, Day 6, biol rep 1, l… ×2 Jurkat cells, sgControl, Day 6, biol rep 2, l… ×2 +10 more

Supports a between-group comparison across 36 samples.

How we read this: 18 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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Metadata from NCBI GEO, cached and refreshed periodically — the NCBI page above is authoritative. Downloads link straight to NCBI/ENA; nothing is proxied through BioTransfer.