Effect of NUDT21 knockdown on gene expression in MUTZ-1 and SKM-1 myelodysplastic syndrome 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)
- Topic
- Myelodysplastic syndromesThis series is part of our curated briefing on it.
- Samples
- 12 samples: 3 × MUTZ-1 cells, shNUDT21 vs 3 × SKM-1 cells, sh control vs 3 × SKM-1 cells, shNUDT21 vs 2 × MUTZ -1cells, sh controlGroups 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 GSE280172_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 PRJNA1176693 and SRA study SRP540469. Searching any of these in the dataset finder brings you back here.
Supports a between-group comparison across 11 samples.
How we read this: 4 replicated groups read from 12 sample titles; they account for 11 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.
- GSM8591131 MUTZ -1cells, sh control-1 MUTZ -1cells, sh control
- GSM8591134 MUTZ -1cells, sh control-2 MUTZ -1cells, sh control
- GSM8591136 MUTZ-1 cells, sh control-3
- GSM8591138 MUTZ-1 cells, shNUDT21-1 MUTZ-1 cells, shNUDT21
- GSM8591140 MUTZ-1 cells, shNUDT21-2 MUTZ-1 cells, shNUDT21
- GSM8591143 MUTZ-1 cells, shNUDT21-3 MUTZ-1 cells, shNUDT21
- GSM8591145 SKM-1 cells, sh control-1 SKM-1 cells, sh control
- GSM8591147 SKM-1 cells, sh control-2 SKM-1 cells, sh control
- GSM8591149 SKM-1 cells, sh control-3 SKM-1 cells, sh control
- GSM8591151 SKM-1 cells, shNUDT21-1 SKM-1 cells, shNUDT21
- GSM8591154 SKM-1 cells, shNUDT21-2 SKM-1 cells, shNUDT21
- GSM8591156 SKM-1 cells, shNUDT21-3 SKM-1 cells, shNUDT21
- GSE276645 The effection of celastrol treatment on SKM-1 cell 6 samples same disease briefing · shares skm-1
- GSE211032 Expression Analysis (RNA-Seq) of adult Myelodysplastic Syndromes (MDS)/Acute Myeloid Leukemia (AML) with isolated monosomy 7 compared to controls 45 samples same disease briefing · shares myelodysplastic
- GSE272173 Molecular profiling of pre-and post-5-azacytidine myelodysplastic syndrome samples identifies predictors of response 34 samples same disease briefing · shares myelodysplastic
- GSE292039 Splicing of erythroid transcription factor is associated with therapeutic response in myelodysplastic syndromes 27 samples same disease briefing · shares myelodysplastic
- GSE237148 Targeting IL-1b–mediated inflammatory signaling overcomes transfusion dependence in early-stage myelodysplastic syndromes 26 samples same disease briefing · shares myelodysplastic
- GSE280881 Rapid Disease Progression of Myelodysplastic Syndrome is Reflected in Transcriptomic and Functional Abnormalities of Bone Marrow MSCs 22 samples same disease briefing · shares myelodysplastic
- GSE290183 Distinct routes of clonal progression in SF3B1-mutant myelodysplastic syndromes 15 samples same disease briefing · shares myelodysplastic
- GSE293014 Identifying clones in myelodysplastic syndromes by using single-cell RNA sequencing 11 samples same disease briefing · shares myelodysplastic
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.