Effect of FOSL1 and HDAC2 knockdown on gene expression in cancer cell lines
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 × H1299 cells, shHDAC2, biol vs 3 × H1299 cells, shControl, biol vs 3 × PANC-1 cells, shFOSL1, biol vs 3 × PANC-1 cells, shControl, biolGroups 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
- Single cell atlas reveals multilayered metabolic heterogeneity across tumour typesEBioMedicine · 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 GSE230729_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 PRJNA962475 and SRA study SRP434823. 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.
- GSM7233175 H1299 cells, shHDAC2, biol rep 1 H1299 cells, shHDAC2, b…
- GSM7233176 H1299 cells, shHDAC2, biol rep 2 H1299 cells, shHDAC2, b…
- GSM7233177 H1299 cells, shHDAC2, biol rep 3 H1299 cells, shHDAC2, b…
- GSM7233178 H1299 cells, shControl, biol rep 1 H1299 cells, shControl,…
- GSM7233179 H1299 cells, shControl, biol rep 2 H1299 cells, shControl,…
- GSM7233180 H1299 cells, shControl, biol rep 3 H1299 cells, shControl,…
- GSM7233181 PANC-1 cells, shFOSL1, biol rep 1 PANC-1 cells, shFOSL1, …
- GSM7233182 PANC-1 cells, shFOSL1, biol rep 2 PANC-1 cells, shFOSL1, …
- GSM7233183 PANC-1 cells, shFOSL1, biol rep 3 PANC-1 cells, shFOSL1, …
- GSM7233184 PANC-1 cells, shControl, biol rep 1 PANC-1 cells, shControl…
- GSM7233185 PANC-1 cells, shControl, biol rep 2 PANC-1 cells, shControl…
- GSM7233186 PANC-1 cells, shControl, biol rep 3 PANC-1 cells, shControl…
- GSE181389 Transcriptome profiling of HOXA13 and HOXB13 expression knockdown in bladder cancer cell lines. 59 samples shares knockdown, lines
- GSE305473 Radiosensitizing effect of THBS1 knockdown in radioresistant head and neck carcinoma cell lines 12 samples shares knockdown, lines
- GSE298581 Global gene expression response to PPARG inhibition in three urothelial cancer cell lines 48 samples shares lines
- GSE273995 Cell-intrinsic platinum response and associated genetic and gene expression signatures in ovarian cancer cell lines and isogenic models 36 samples shares lines
- GSE274006 Cell-intrinsic platinum response and associated genetic and gene expression signatures in ovarian cancer cell lines and isogenic models [isogenic models] 33 samples shares lines
- GSE251958 Predicting patient outcome based on gene-expression biomarkers learned from colorectal cancer organoids and cell lines 21 samples shares lines
- GSE225645 Hypoxia-induced gene expression profiling of esophageal cancer cell lines 12 samples shares lines
- GSE232322 Differential gene expression in breast cancer cell lines treated with a Baicalein at 100 uM concentration 12 samples shares lines
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.