Transcriptomes of UFMylation gene knockdown in mouse and human cells treated with hypoxia
RNA-seq (gene expression) · human · 15 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
- 15 samples: 6 × sgL1 vs 3 × sgCtrl vs 3 × KO vs 3 × NCGroups 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 GSE272937_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 PRJNA1139426 and SRA study SRP521863. Searching any of these in the dataset finder brings you back here.
Supports a between-group comparison across 15 samples.
How we read this: 4 replicated groups read from 15 sample titles; they account for 15 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.
- GSM8415325 sgL1_1 sgL1
- GSM8415326 sgL1_2 sgL1
- GSM8415327 sgL1_3 sgL1
- GSM8415328 sgL1_4 sgL1
- GSM8415329 sgL1_5 sgL1
- GSM8415330 sgL1_6 sgL1
- GSM8415331 sgCtrl_1 sgCtrl
- GSM8415332 sgCtrl_2 sgCtrl
- GSM8415333 sgCtrl_3 sgCtrl
- GSM8415334 KO_1 KO
- GSM8415335 KO_2 KO
- GSM8415336 KO_3 KO
- GSM8415337 NC_1 NC
- GSM8415338 NC_2 NC
- GSM8415339 NC_3 NC
- GSE260725 Individual RNA-seq for different prostate cancer cells and Lucap35CR PDX treated by SR8278,JQ1,AZD5153,ENZ or by FOXA1 and NR1D1 gene knockdown or NR1D1 overexpression. 26 samples shares knockdown, treated
- GSE241264 Gene expression changes in human pluripotent and fibroblast cells and mouse embryonic fibroblasts upon NORAD lncRNA knockdown 34 samples shares knockdown
- GSE236107 Single cell transcriptomic analysis of acute and early ART-treated HIV-1-infected CD4+T cells from a reservoir-marking humanized mouse model 14 samples shares treated
- GSE259220 Cas13bt3 knockdown of VEGFA mRNA in mammalian cells and mouse retina [RNA-Seq] 61 samples shares knockdown
- GSE303378 Transcriptomic profiling of bone marrow cells from CML mouse models and newly diagnosed patients treated with SOS1 inhibitor BI-3406 and/or imatinib 48 samples shares treated
- GSE333739 RNA-seq of human HN-SCC-151 HPV-negative head and neck squamous cell carcinoma cells treated with DMSO or the SUV420H1 inhibitor A-196/siNC (control) or siSUV420H1 siRNAs. 21 samples shares treated
- GSE333415 Single-cell transcriptomic effects of LOX knockdown on tumor cell xenografts implanted on aged mouse breast dECM scaffolds 12 samples shares knockdown
- GSE282690 Single cell gene expression profiling of splenic cells in mice treated with gated CD33-CD123 CARs compared to those with conventional CD123 CAR expression 5 samples shares treated
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.