Highly-metastatic colorectal cancer cell released Nidogen 1-Enriched Extracellular Vesicles promote liver metastasis by activating hepatic stellate cells and forming the neutrophilextracellulartraps
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)
- Topic
- Colorectal cancerThis series is part of our curated briefing on it.
- Samples
- 18 samples: 6 conditions, mostly in triplicateGroups 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 GSE263027_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 PRJNA1095473 and SRA study SRP499406. Searching any of these in the dataset finder brings you back here.
Supports a between-group comparison across 18 samples.
How we read this: 6 replicated groups read from 18 sample titles; they account for 18 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.
- GSM8183589 SW480-P-1 SW480-P
- GSM8183590 SW480-P-2 SW480-P
- GSM8183591 SW480-P-3 SW480-P
- GSM8183592 SW480-LM3-1 SW480-LM3
- GSM8183593 SW480-LM3-2 SW480-LM3
- GSM8183594 SW480-LM3-3 SW480-LM3
- GSM8183595 EV-XP-LX-2-1 EV-XP-LX-2
- GSM8183596 EV-XP-LX-2-2 EV-XP-LX-2
- GSM8183597 EV-XP-LX-2-3 EV-XP-LX-2
- GSM8183598 EV-XP-NID1-LX-2-1 EV-XP-NID1-LX-2
- GSM8183599 EV-XP-NID1-LX-2-2 EV-XP-NID1-LX-2
- GSM8183600 EV-XP-NID1-LX-2-3 EV-XP-NID1-LX-2
- GSM8183601 LV5-1 LV5
- GSM8183602 LV5-2 LV5
- GSM8183603 LV5-3 LV5
- GSM8183604 LV5-NID1-1 LV5-NID1
- GSM8183605 LV5-NID1-2 LV5-NID1
- GSM8183606 LV5-NID1-3 LV5-NID1
- GSE250000 Bulk RNA-sequencing of transduced colorectal cancer cell line HCT-116 and breast cancer cell line MCF-7 overexpressing full-lenght p53β or p53β-stop-lost. 4 samples same disease briefing · shares colorectal
- GSE12032 Inherent gene signature of stage II and III colorectal cancer leads in individual recurrence 198 samples same disease briefing · shares colorectal
- GSE109308 Single-cell transcriptomic survey of adenomatous polyposis patients with germline APC mutations 97 samples same disease briefing
- GSE110009 Single cell transcriptome landscape of primary and metastatic tumor in colon cancer 76 samples same disease briefing
- GSE289930 Proteogenomic Characterization of Primary Oral Cancer Unveils Extracellular Matrix Remodeling and Immunosuppressive Microenvironment Linked to Lymph Node Metastasis [RNA-seq] 33 samples shares extracellular, metastasis
- GSE309392 Cancer-associated fibroblasts promote esophageal carcinogenesis and lung metastasis by CDH11-mediated extracellular matrix environment remodeling [scRNA-Seq] 23 samples shares extracellular, metastasis
- GSE294455 Sphingolipids in extracellular vesicles released from the skeletal muscle plasma membrane control muscle stem cell fate during muscle regeneration 10 samples shares extracellular, released
- GSE255775 Transcriptomic Profiling of Plasma Extracellular Vesicles Enables Reliable Annotation of the Cancer-specific Transcriptome and Molecular Subtype 319 samples shares extracellular
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.