GEO series

Coordination of nuclear RNA processing by speckle-localized kinase TAOK2

GSE318441 Homo sapiens (human) RNA-seq (gene expression) 24 samples Submitted 2026/02/05 Platform GPL18573Platform GPL24676

At a glance

RNA-seq (gene expression) · human · 24 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: 24 samples: 10 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)

Nuclear speckles are membraneless organelles that act as active splicing hubs especially at sites of high transcription. Emerging views of this dynamic subnuclear structure place it as a hub of RNA processing, impacting steps from transcription to export. To manage this complex microcosm of RNA metabolism, nuclear speckles also require kinases and phosphorylation to execute their functions.

Read the full summary ↓

The nuclear speckle-localized kinase, TAOK2, mediates the splicing and export of viral transcripts at the nuclear speckle, but its role in the processing of cellular transcripts was unknown. We used siRNA knockdown of TAOK2 and assessed RNA transcripts in both whole cell and nucleocytoplasmic fractions to characterize the complete endogenous effects of TAOK2. We found that TAOK2 knockdown impacts over 10% of the transcriptome, through changes in alternative splicing, export and transcript abundance. Cellular and biochemical phosphoproteomics further revealed nuclear speckle scaffolding proteins SRRM1 and SRRM2 as potential direct phosphorylation targets of TAOK2, mediating its large effects on speckle integrity and speckle-localized splicing. Indeed, knockdown of TAOK2 perturbs almost all speckle-resident serine/arginine (SR)-rich proteins while leaving heterogeneous ribonucleoproteins unperturbed. Altogether, we propose that phosphorylation of SRRM1/2 by TAOK2 plays a structural maintenance role that impacts SR protein-driven exon inclusion at the nuclear speckle.

This dataset

Open GSE318441 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 GSE318441_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 PRJNA1418735 and SRA study SRP674635. Searching any of these in the dataset finder brings you back here.

NCBI GEO page ↗

Study design

10 conditions, mostly in duplicate

con_mock ×3 taok2_mock ×3 dmso_mock ×3 c2_mock ×3 taok2kd_cyto_S ×2 taok2kd_nuc_S ×2 taok2kd_total_S ×2 wt_cyto_S ×2 +2 more

Supports a between-group comparison across 24 samples.

How we read this: 10 replicated groups read from 24 sample titles; they account for 24 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

GSM9494909 taok2kd_cyto_S1 taok2kd_cyto_S
GSM9494910 taok2kd_cyto_S2 taok2kd_cyto_S
GSM9494911 taok2kd_nuc_S1 taok2kd_nuc_S
GSM9494912 taok2kd_nuc_S2 taok2kd_nuc_S
GSM9494913 taok2kd_total_S1 taok2kd_total_S
GSM9494914 taok2kd_total_S2 taok2kd_total_S
GSM9494915 wt_cyto_S1 wt_cyto_S
GSM9494916 wt_cyto_S2 wt_cyto_S
GSM9494917 wt_nuc_S1 wt_nuc_S
GSM9494918 wt_nuc_S2 wt_nuc_S
GSM9494919 wt_total_S1 wt_total_S
GSM9494920 wt_total_S2 wt_total_S
GSM9494921 con_mock_1 con_mock
GSM9494922 con_mock_2 con_mock
GSM9494923 con_mock_3 con_mock
GSM9494924 taok2_mock_1 taok2_mock
GSM9494925 taok2_mock_2 taok2_mock
GSM9494926 taok2_mock_3 taok2_mock
GSM9494927 dmso_mock_1 dmso_mock
GSM9494928 dmso_mock_2 dmso_mock
GSM9494929 dmso_mock_3 dmso_mock
GSM9494930 c2_mock_1 c2_mock
GSM9494931 c2_mock_2 c2_mock
GSM9494932 c2_mock_3 c2_mock

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GSE277571 Nuclear Protein Aggregates Disrupt RNA Processing and Alter Biomechanics in a Muscle Cell Model of OPMD 18 samples shares processing, nuclear
GSE264304 Nuclear Speckles enable processing of RNA from GC-rich Isochores [SON_Halo_Fractionation] 18 samples shares processing, nuclear
GSE260934 Coordination between the eIF2 kinase GCN2 and p53 signaling supports purine metabolism and the progression of prostate cancer 16 samples shares coordination, kinase
GSE264307 Nuclear Speckles enable processing of RNA from GC-rich Isochores [SON_Halo_SRRM2_dTAG_pA] 12 samples shares processing, nuclear
GSE310859 Nuclear Speckles enable processing of RNA from GC-rich Isochores [4sU] 8 samples shares processing, nuclear
GSE264297 Nuclear Speckles enable processing of RNA from GC-rich Isochores [HCT116_wt_TRA2AB_KD_pA] 6 samples shares processing, nuclear

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