RNA-seq of HeLa cells and RPE1 cells after USP39 KD using RNAi
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: 3 × RNA-seq, HeLa, USP39, Ctrl, vs 3 × RNA-seq, HeLa, USP39, KD, vs 3 × RNA-seq_RPE_Ctrl vs 3 × RNA-seq_RPE_USP39_KDGroups 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
- Pathogenic proteotoxicity of cryptic splicing is alleviated by ubiquitination and ER-phagyScience (New York, N.Y.) · 2024
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 GSE229329_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 PRJNA954019 and SRA study SRP431817. Searching any of these in the dataset finder brings you back here.
Supports a between-group comparison across 12 samples.
How we read this: 4 replicated groups read from 12 sample titles; they account for 12 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.
- GSM7158895 RNA-seq, HeLa, USP39, Ctrl, rep1 RNA-seq, HeLa, USP39, C…
- GSM7158896 RNA-seq, HeLa, USP39, Ctrl, rep2 RNA-seq, HeLa, USP39, C…
- GSM7158897 RNA-seq, HeLa, USP39, KD, rep1 RNA-seq, HeLa, USP39, K…
- GSM7158898 RNA-seq, HeLa, USP39, KD, rep2 RNA-seq, HeLa, USP39, K…
- GSM7158899 RNA-seq, HeLa, USP39, KD, rep3 RNA-seq, HeLa, USP39, K…
- GSM7325125 RNA-seq, HeLa, USP39, Ctrl, rep3 RNA-seq, HeLa, USP39, C…
- GSM8157263 RNA-seq_RPE_Ctrl_rep1 RNA-seq_RPE_Ctrl
- GSM8157264 RNA-seq_RPE_Ctrl_rep2 RNA-seq_RPE_Ctrl
- GSM8157265 RNA-seq_RPE_Ctrl_rep3 RNA-seq_RPE_Ctrl
- GSM8157266 RNA-seq_RPE_USP39_KD_rep1 RNA-seq_RPE_USP39_KD
- GSM8157267 RNA-seq_RPE_USP39_KD_rep2 RNA-seq_RPE_USP39_KD
- GSM8157268 RNA-seq_RPE_USP39_KD_rep3 RNA-seq_RPE_USP39_KD
- GSE278951 Genome-wide DNA replication profiling and full-length total RNA sequencing from the same single cell [hTERT-RPE1 Whole-S] 98 samples shares rpe1
- GSE222556 Neoadjuvant PARPi or Chemotherapy in Ovarian Cancer Informs Targeting Effector Treg Cells for Homologous-Recombination-Deficient Tumors [10x scRNA-seq] 67 samples shares rna-seq
- GSE282444 Epigenetic Memory of Intestinal Epithelial Cells in Inflammatory Bowel Disease [RNA-seq] 56 samples shares rna-seq
- GSE319641 RNA-Seq profiling of pre- and on-treatment tumor samples from breast cancer patients enrolled in the NeoTRIP trial. 401 samples shares rna-seq
- GSE287301 Single-cell RNA-sequencing of HNSCC-infiltrating T cells 48 samples shares rna-seq
- GSE334923 Single-cell RNA-seq atlas of peripheral blood and kidney graft immune cells in chronic antibody-mediated rejection 48 samples shares rna-seq
- GSE205154 Bulk RNA-Seq gene expression data for 289 primary and metastatic pancreatic ductal adenocarcinoma (PDAC) tumor samples from FFPE blocks. 289 samples shares rna-seq
- GSE294300 Single-cell gene expression profiles of cells from primary colorectal cancer and adjacent normal tissue [scRNA-Seq] 36 samples shares rna-seq
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.