RNA-Seq analysis of b-catenin over expression in Human liver cancer cells
RNA-seq (gene expression) · human · 18 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
- 18 samples: 18 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 GSE190488_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 PRJNA787594 and SRA study SRP350049. 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 18 sample titles: 18 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.
- GSM5724560 Huh7 Cells b-catenin (Replicate_1)
- GSM5724561 Huh7 Cells b-catenin (Replicate_2)
- GSM5724562 Huh7 Cells b-catenin (Replicate_3)
- GSM5724563 Huh7 Cells vector (Replicate_1)
- GSM5724564 Huh7 Cells vector (Replicate_2)
- GSM5724565 Huh7 Cells vector (Replicate_3)
- GSM5724566 SNU-387 Cells b-catenin (Replicate_1)
- GSM5724567 SNU-387 Cells b-catenin (Replicate_2)
- GSM5724568 SNU-387 Cells b-catenin (Replicate_3)
- GSM5724569 SNU-387 Cells vector (Replicate_1)
- GSM5724570 SNU-387 Cells vector (Replicate_2)
- GSM5724571 SNU-387 Cells vector (Replicate_3)
- GSM5724572 SNU-475 Cells b-catenin (Replicate_1)
- GSM5724574 SNU-475 Cells b-catenin (Replicate_2)
- GSM5724575 SNU-475 Cells b-catenin (Replicate_3)
- GSM5724576 SNU-475 Cells vector (Replicate_1)
- GSM5724577 SNU-475 Cells vector (Replicate_2)
- GSM5724578 SNU-475 Cells vector (Replicate_3)
- GSE303271 RNA-seq of liver biopsies from patients with pediatric autoimmune liver disease 64 samples shares rna-seq, liver
- GSE202379 Single Nuclei RNA-Seq to map progression of non-alcoholic fatty liver disease (NAFLD) in patients II 59 samples shares rna-seq, liver
- GSE210077 Single nuclei RNA-sequencing of normal and diseased liver 40 samples shares rna-seq, liver
- GSE294300 Single-cell gene expression profiles of cells from primary colorectal cancer and adjacent normal tissue [scRNA-Seq] 36 samples shares rna-seq
- GSE292858 RNA-Seq analysis of tumor and matched normal samples from colorectal cancer patients. 73 samples shares rna-seq
- GSE222556 Neoadjuvant PARPi or Chemotherapy in Ovarian Cancer Informs Targeting Effector Treg Cells for Homologous-Recombination-Deficient Tumors [10x scRNA-seq] 67 samples shares rna-seq
- GSE319641 RNA-Seq profiling of pre- and on-treatment tumor samples from breast cancer patients enrolled in the NeoTRIP trial. 401 samples shares rna-seq
- GSE297041 Chemoradiation Reprograms Tumor Cells and Immune Microenvironment In Cervical Cancer [scRNA-seq] 18 samples shares rna-seq
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.