Effect of depletion of ZFC3H1, PABPN1 and CNOT4 on gene expression in human cells.
RNA-seq (gene expression) · human · 12 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
- 12 samples: 12 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.
- Paper
- Nuclear effects play an important role in determining codon usage-dependent human gene expressionNature communications · 2025
Read the full summary ↓
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.
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.
Supplementary files
The count tables and other files the authors uploaded. Take only the samples you need, or the whole study as GSE261505_RAW.tar (it can run to tens of gigabytes).
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.
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 PRJNA1087339 and SRA study SRP495032. Searching any of these in the dataset finder brings you back here.
Any grouping that defines a comparison lives in the sample characteristics, which GEO records separately from the titles.
How we read this: Read from 12 sample titles: 12 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.
- GSM8145427 HEK 293 cells, siControl-Total RNA
- GSM8145428 HEK 293 cells, siControl-Cytosolic RNA
- GSM8145429 HEK 293 cells, siControl-Nuclear RNA
- GSM8145430 HEK 293 cells, siZFC3H1-Total RNA
- GSM8145431 HEK 293 cells, siZFC3H1-Cytosolic RNA
- GSM8145432 HEK 293 cells, siZFC3H1-Nuclear RNA
- GSM8145433 HEK 293 cells, siPABPN1-Total RNA
- GSM8145434 HEK 293 cells, siPABPN1-Cytosolic RNA
- GSM8145435 HEK 293 cells, siPABPN1-Nuclear RNA
- GSM8145436 HEK 293 cells, siCNOT4-Total RNA
- GSM8145437 HEK 293 cells, siCNOT4-Cytosolic RNA
- GSM8145438 HEK 293 cells, siCNOT4-Nuclear RNA
- GSE277237 Auxin-induced depletion of human CCR4-NOT subunits reveals opposing functions of CNOT1 and CNOT4 in mRNA metabolism 48 samples shares cnot4, depletion
- GSE224414 Effect of depletion of SPAST exon17 on gene expression in human embryonic stem cells (hESC) and cortical organoids (COs) 12 samples shares depletion
- GSE291063 Gene expression profiling of human DLD-1 cells after instant depletion of TREX2 subunits 90 samples shares depletion
- GSE217204 Effect of depletion of HIF-1α, FACT or RNF20/40 on gene expression in hypoxia of MCF7 breast cancer cells 24 samples shares depletion
- GSE289091 Effects of mechanical stretch and depletion of lamin A/C on gene expression in human myotubes (RNAseq) 18 samples shares depletion
- GSE265772 Effect of depletion of IMPDH1 and IMPDH2 on gene expression after DNA damage in HeLa cells 18 samples shares depletion
- GSE264653 Effect of MITF depletion on gene expression in U2OS cells 18 samples shares depletion
- GSE265998 Effect of DHX29, GIGYF2, 4EHP, and DHX29/4EHP depletion on gene expression in K562 cells 15 samples shares depletion
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.