The regulation of transcriptome in HCC cells by KDM1A [HepG2_shKDM1A_RNAseq]
RNA-seq (gene expression) · human · 3 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
- 3 samples
- 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
- Transposable elements-mediated recruitment of KDM1A epigenetically silences HNF4A expression to promote hepatocellular carcinomaNature communications · 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 GSE228075_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 PRJNA947988 and SRA study SRP428949. Searching any of these in the dataset finder brings you back here.
The sample list for this study is not cached yet. Press Load samples and it will be fetched from NCBI.
+ 3 more — browse all 3 samples with per-sample file links →
- GSE228074 The epigenetic regulatory role of KDM1A in HCC cells [HepG2_shKDM1A_CUTTag_seq] 11 samples shares shkdm1a, kdm1a, hepg2, hcc
- GSE287572 Transcriptome analysis of triple-negative breast cancer cells HCC1937 and MDA-MB-231 treated with Kalanchoe pinnata (Bryophyllum pinnata) reveals regulation of migration and invasion by downregulation of genes JAK2, ROCK1, ROCK2 and PIK3CA. 12 samples shares hcc
- GSE283054 Digital transformation of herbal medicine: Conversion to biological entity data using Qi related decoction and constituent herbal medicine-induced transcriptome sequencing_third_HepG2 270 samples shares hepg2
- GSE244707 Digital transformation of herbal medicine: Conversion to biological entity data using tonifying herbal medicine-induced transcriptome sequencing_Tonifying_HepG2 270 samples shares hepg2
- GSE248976 Digital transformation of herbal medicine: Conversion to biological entity data using digestive herbal medicine-induced transcriptome sequencing_second_HepG2 267 samples shares hepg2
- GSE299063 Large scale cell-based transcriptome data treated with Jakyakgamcho-tang in HepG2 cell 168 samples shares hepg2
- GSE270357 Transcriptome sequencing of palmitic acid-treated HepG2 cells upon intervention of curcumin or curcumin-copper complex 9 samples shares hepg2
- GSE302559 Transcriptomic points of departure for 6PPD-Quinone derived from human Caco-2 and HepG2 cells 72 samples shares hepg2
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.