Ubiquitin-like proteins NEDD8 and SUMO2 control epithelial homeostasis, regeneration, and inflammation [RNA-Seq]
RNA-seq (gene expression) · human · 8 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
- 8 samples: 2 × A431_DMSO vs 2 × A431_NEDD8i vs 2 × CAL27_DMSO vs 2 × CAL27_NEDD8iGroups 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.
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 GSE326487_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 PRJNA1445702 and SRA study SRP687979. Searching any of these in the dataset finder brings you back here.
Supports a between-group comparison across 8 samples.
How we read this: 4 replicated groups read from 8 sample titles; they account for 8 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.
- GSM9632709 A431_DMSO_1 A431_DMSO
- GSM9632710 A431_DMSO_2 A431_DMSO
- GSM9632711 A431_NEDD8i_1 A431_NEDD8i
- GSM9632712 A431_NEDD8i_2 A431_NEDD8i
- GSM9632713 CAL27_DMSO_1 CAL27_DMSO
- GSM9632714 CAL27_DMSO_2 CAL27_DMSO
- GSM9632715 CAL27_NEDD8i_1 CAL27_NEDD8i
- GSM9632716 CAL27_NEDD8i_2 CAL27_NEDD8i
- GSE328185 Ubiquitin-like proteins NEDD8 and SUMO2 control epithelial homeostasis, regeneration, and inflammation [RNA-Seq epithelial] 12 samples shares nedd8, sumo2, ubiquitin-like, regeneration, homeostasis, epithelial, proteins, control
- GSE276073 Targeting SUMO2 reverses aberrant epigenetic rewiring driven by SS18::SSX fusion oncoproteins and impairs sarcomagenesis [RNA-seq] 12 samples shares sumo2, proteins
- GSE276074 Targeting SUMO2 reverses aberrant epigenetic rewiring driven by SS18::SSX fusion oncoproteins and impairs sarcomagenesis 30 samples shares sumo2, proteins
- GSE276071 Targeting SUMO2 reverses aberrant epigenetic rewiring driven by SS18::SSX fusion oncoproteins and impairs sarcomagenesis [CUT&RUN] 6 samples shares sumo2, proteins
- GSE276068 Targeting SUMO2 reverses aberrant epigenetic rewiring driven by SS18::SSX fusion oncoproteins and impairs sarcomagenesis [ChIP-seq] 6 samples shares sumo2, proteins
- GSE294455 Sphingolipids in extracellular vesicles released from the skeletal muscle plasma membrane control muscle stem cell fate during muscle regeneration 10 samples shares regeneration, control
- GSE287209 A human organoid model of alveolar regeneration reveals distinct epithelial responses to interferon-gamma 3 samples shares regeneration, epithelial
- GSE277084 Transcriptome-based screening in TARDBP/TDP-43 knock-in motor neurons identifies the NEDD8-activating enzyme inhibitor MLN4924 [RNA-Seq] 15 samples shares nedd8
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.