Alterations of splicing and gene expression in IMR90 Control cells and IMR90 RAS cells upon knockdown of SF3B1.
RNA-seq (gene expression) · human · 24 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
- 24 samples: 24 samples, each with a distinct title — no replicated groupsGroups 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 GSE209624_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 PRJNA861848 and SRA study SRP387835. Searching any of these in the dataset finder brings you back here.
Any grouping that defines a comparison lives in the sample characteristics, which GEO records separately from the titles.
How we read this: Read from 24 sample titles: 24 distinct titles with little repetition. 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.
- GSM6380794 IMR90 Control siNT1 Rep 1 [EV_1_siNT1]
- GSM6380795 IMR90 Control siNT1 Rep 2 [EV_2_siNT1]
- GSM6380796 IMR90 Control siNT1 Rep 3 [EV_4_siNT1]
- GSM6380797 IMR90 Control siNT2 Rep 1 [EV_2_siNT2]
- GSM6380798 IMR90 Control siNT2 Rep 2 [EV_3_siNT2]
- GSM6380799 IMR90 Control siNT2 Rep 3 [EV_4_siNT2]
- GSM6380800 IMR90 Control siSF3B1_13 Rep 1 [EV_2_SF3B1_13]
- GSM6380801 IMR90 Control siSF3B1_13 Rep 2 [EV_3_SF3B1_13]
- GSM6380802 IMR90 Control siSF3B1_13 Rep 3 [EV_4_SF3B1_13]
- GSM6380803 IMR90 Control siSF3B1_16 Rep 1 [EV_1_SF3B1_16]
- GSM6380804 IMR90 Control siSF3B1_16 Rep 2 [EV_2_SF3B1_16]
- GSM6380805 IMR90 Control siSF3B1_16 Rep 3 [EV_3_SF3B1_16]
- GSM6380806 IMR90 RAS siNT1 Rep 1 [iRas_3_siNT1]
- GSM6380807 IMR90 RAS siNT1 Rep 2 [iRas_4_siNT1]
- GSM6380808 IMR90 RAS siNT1 Rep 3 [iRas_5_siNT1]
- GSM6380809 IMR90 RAS siNT2 Rep 1 [iRas_3_siNT2]
- GSM6380810 IMR90 RAS siNT2 Rep 2 [iRas_4_siNT2]
- GSM6380811 IMR90 RAS siNT2 Rep 3 [iRas_5_siNT2]
- GSM6380812 IMR90 RAS siSF3B1_13 Rep 1 [iRas_2_SF3B1_13]
- GSM6380813 IMR90 RAS siSF3B1_13 Rep 2 [iRas_4_SF3B1_13]
- GSM6380814 IMR90 RAS siSF3B1_13 Rep 3 [iRas_5_SF3B1_13]
- GSM6380815 IMR90 RAS siSF3B1_16 Rep 1 [iRas_1_SF3B1_16]
- GSM6380816 IMR90 RAS siSF3B1_16 Rep 2 [iRas_3_SF3B1_16]
- GSM6380817 IMR90 RAS siSF3B1_16 Rep 3 [iRas_5_SF3B1_16]
- GSE304266 Bulk RNA‑seq of IMR90 fibroblasts in IR‑induced senescence with siRNA knockdowns of CCND1, CDK4, CDK6 and controls 21 samples shares imr90, knockdown, control
- GSE338135 NRAS knockdown reverses monocytic cell state and resensitizes resistant FLT3-AML cells to gilteritinib 75 samples shares ras, knockdown
- GSE285698 DNA topological regulation by topoisomerase IIβ-DNA-PK interaction is important for controlled hypoxia-inducible gene expression [RNA-Seq] 12 samples shares ras, control
- GSE277500 Coordinated control of genome-nuclear lamina interactions by Topoisomerase 2B and Lamin B receptor (pA-DamID) 226 samples shares ras, control
- GSE243499 Mutant FOXO1 Controls an Oncogenic Network via Enhancer Accessibility and RNA Polymerase Pause Release 79 samples shares ras, control
- GSE220318 Splicing Factor RBM22 Broadly Affects RNA Polymerase II 5' Pausing, Elongation Rate and Termination and Prevents Genome Instability 70 samples shares ras, splicing
- GSE288172 Influence of NIPBL Knockdown-Induced Alterations in Cohesin Loop Extrusion on CTCF Loops, Enhancer-Promoter Connectivity, and PRC Domain Contacts During hESC Differentiation into Pancreatic Lineages 263 samples shares alterations, knockdown
- GSE264120 Trastuzumab-associated cardiotoxicity in Patient Specific iPSC-derived cardiomyocytes from HER2+ breast cancer patients 74 samples shares ras
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.