Transcriptomic analysis of the diethylnitrosamine (DEN)-induced HCC mRNA from Pck1 KO and WT mice
RNA-seq (gene expression) · mouse · 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
- Mus musculus (mouse)
- Samples
- 12 samples: 5 × WT vs 3 × KO vs 3 × koGroups 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 GSE202618_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 PRJNA836784 and SRA study SRP374519. Searching any of these in the dataset finder brings you back here.
Supports a between-group comparison across 11 samples.
How we read this: 3 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.
- GSM6125826 KO1354 KO
- GSM6125827 KO1361 KO
- GSM6125828 KO67 KO
- GSM6125829 ko1828 ko
- GSM6125830 ko1831 ko
- GSM6125831 ko1937 ko
- GSM6125832 KP5
- GSM6125833 WT1 WT
- GSM6125834 WT1359 WT
- GSM6125835 WT1838 WT
- GSM6125836 WT2 WT
- GSM6125837 WT3 WT
- GSE283382 N6-methyladenosine modulate second cell fate decision by enhancing mRNA stability of pivotal transcription factors during primitive endoderm development [TBLC_RNAseq] 98 samples shares den, mrna
- GSE302657 Regulation of mRNA polyadenylation governs body plan formation in gastruloids 60 samples shares den, mrna
- GSE237643 Deletion of the mRNA endonuclease Regnase-1 promotes NK cell anti-tumor activity via OCT2- dependent transcription of Ifng 58 samples shares den, mrna
- GSE309228 Radiation induced YTHDF2 in dendritic cells impairs antitumor immunity 45 samples shares den, induced
- GSE300288 Single-cell and spatial transcriptomics analysis of tobacco-associated lung adenocarcinoma development, and in response to targeting inflammation alone or in combination with immune checkpoint blockade in precancerous phase [scRNA-seq] 31 samples shares den
- GSE325548 Time-resolved transcriptomic profiling of surgical wounds identifies stage-specific therapeutic targets for residual ovarian cancer 48 samples shares den
- GSE255004 Sensory Flicker Stimulation of 5xFAD Mice Activates Immune Pathways in a Frequency and Time Dependent Manner 176 samples shares den
- GSE287323 Transcriptomic profiling of oligodendrocytes, astrocytes, and microglia in an experimental autoimmune encephalomyelitis (EAE) model of demyelination 19 samples shares den
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.