Effect of 4-HDHA during TNF-induced HT-29 cells apoptosis
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: 12 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.
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 GSE249870_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 PRJNA1051062 and SRA study SRP477319. 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 12 sample titles: 12 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.
- GSM7966198 HT-29 cells,control,replicate1 [C1]
- GSM7966199 HT-29 cells,control,replicate2 [C2]
- GSM7966200 HT-29 cells,control,replicate3 [C3]
- GSM7966201 HT-29 cells,control+4-HDHA,replicate1 [CH1]
- GSM7966202 HT-29 cells,control+4-HDHA,replicate2 [CH2]
- GSM7966203 HT-29 cells,control+4-HDHA,replicate3 [CH3]
- GSM7966204 HT-29 cells,TNF-a,replicate1 [T1]
- GSM7966205 HT-29 cells,TNF-a,replicate2 [T2]
- GSM7966206 HT-29 cells,TNF-a,replicate3 [T3]
- GSM7966207 HT-29 cells,TNF-a+4-HDHA,replicate1 [TH1]
- GSM7966208 HT-29 cells,TNF-a+4-HDHA,replicate2 [TH2]
- GSM7966209 HT-29 cells,TNF-a+4-HDHA,replicate3 [TH3]
- GSE248867 Effect of ferrostatin-1 and liproxstatin-1 during TNF-induced HT-29 cells apoptosis 14 samples shares ht-29, tnf-induced, apoptosis
- GSE337619 Differential Transcriptomic Responses to MRQ 74 and MRQ 76 Rice Extracts in HT-29 Cells; Implications for Apoptosis and Cell Cycle Regulation 8 samples shares ht-29, apoptosis
- GSE320366 Short-Duration HIPEC-Mimetic Exposure to Mithramycin A Induces Structured Transcriptional Reprogramming in HT-29 Colorectal Cancer Cells 8 samples shares ht-29
- GSE301483 HT-29 cells exposed to lead ion by transcriptome 6 samples shares ht-29
- GSE90944 RNA-seq in HT-29 colorectal cancer cells after F. nucleatum treatment 6 samples shares ht-29
- GSE284658 HT-29 and SW620 24 samples shares ht-29
- GSE276336 ZEB1-mediated Epithelial to Mesenchymal Transition in Colorectal cancer HT-29 cell line 6 samples shares ht-29
- GSE250393 Transcriptomic effects of caspase cleavage at TFIIB residue D207 during apoptosis and KSHV infection [TFIIB(D207A)] 32 samples shares apoptosis
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.