Global alteration of transcript decay rates upon ZNF598 knockdown
RNA-seq (gene expression) · human · 22 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
- 22 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.
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 GSE233374_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 PRJNA975953 and SRA study SRP439406. Searching any of these in the dataset finder brings you back here.
Supports a between-group comparison across 20 samples.
How we read this: 10 replicated groups read from 22 sample titles; they account for 20 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.
- GSM7426470 BRIC_shControl_0h_rep1 BRIC_shControl_0h
- GSM7426471 BRIC_shControl_0h_rep2 BRIC_shControl_0h
- GSM7426472 BRIC_shZNF598_0h_rep1 BRIC_shZNF598_0h
- GSM7426473 BRIC_shZNF598_0h_rep2 BRIC_shZNF598_0h
- GSM7426474 BRIC_shControl_2h_rep1 BRIC_shControl_2h
- GSM7426475 BRIC_shControl_2h_rep2 BRIC_shControl_2h
- GSM7426476 BRIC_shZNF598_2h_rep1 BRIC_shZNF598_2h
- GSM7426477 BRIC_shZNF598_2h_rep2 BRIC_shZNF598_2h
- GSM7426478 BRIC_shControl_4h_rep1 BRIC_shControl_4h
- GSM7426479 BRIC_shControl_4h_rep2 BRIC_shControl_4h
- GSM7426480 BRIC_shZNF598_4h_rep1 BRIC_shZNF598_4h
- GSM7426481 BRIC_shZNF598_4h_rep2 BRIC_shZNF598_4h
- GSM7426482 BRIC_shControl_6h_rep1 BRIC_shControl_6h
- GSM7426483 BRIC_shControl_6h_rep2 BRIC_shControl_6h
- GSM7426484 BRIC_shZNF598_6h_rep1 BRIC_shZNF598_6h
- GSM7426485 BRIC_shZNF598_6h_rep2 BRIC_shZNF598_6h
- GSM7426486 BRIC_shControl_10h_rep1 BRIC_shControl_10h
- GSM7426487 BRIC_shControl_10h_rep2 BRIC_shControl_10h
- GSM7426488 BRIC_shZNF598_10h_rep1 BRIC_shZNF598_10h
- GSM7426489 BRIC_shZNF598_10h_rep2 BRIC_shZNF598_10h
- GSM7426490 BRIC_shControl_24h_rep1
- GSM7426491 BRIC_shZNF598_24h_rep1
- GSE178411 Whole-transcriptome analysis illustrates evolving transcriptional human response to injury in acute wounds and scars 108 samples shares transcript, rates
- GSE342032 Isoform-selective antisense oligonucleotide knockdown of SNCA-dIRE and SNCA-IRE transcripts in SK-MEL-28 cells (dose-response) 36 samples shares transcript, knockdown
- GSE314310 Cardiopedia-Ligand: a Ligand Stimulation Atlas for Cardiac Function and Transcriptional Response 468 samples shares transcript
- GSE205672 Transcriptomes of human PBMCs and monocytes in sepsis patients 460 samples shares transcript
- GSE264667 Transcriptome-wide characterization of genetic perturbations 224 samples shares transcript
- GSE263733 Single-cell transcriptome analysis reveals subtype-specific clonal evolution and microenvironmental changes in liver metastasis of pancreatic adenocarcinoma and their clinical implications 218 samples shares transcript
- GSE135251 TRANSCRIPTOMIC PROFILING ACROSS THE SPECTRUM OF NON-ALCOHOLIC FATTY LIVER DISEASE 216 samples shares transcript
- GSE310058 Single-nucleus transcriptomic profiling of human lung tissue in chronic obstructive pulmonary disease (COPD) [snRNA-seq] 149 samples shares transcript
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.