Effect of genetic modification of extracellular matrix-related genes on B16F1 melanoma progression
RNA-seq (gene expression) · mouse · 15 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
- 15 samples: 11 distinct titles, 2 of them repeatedGroups 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
- Loss of the extracellular protease ADAMTS1 reveals an antitumorigenic program involving the action of NIDOGEN-1 on macrophage polarizationOncoimmunology · 2025
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 GSE271194_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 PRJNA1130440 and SRA study SRP517287. Searching any of these in the dataset finder brings you back here.
How we read this: Read from 15 sample titles: 11 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.
- GSM8371600 B16F1 tumor 1, day 21
- GSM8371601 B16F1 tumor 2, day 21
- GSM8371602 B16F1 tumor 3, day 21
- GSM8371603 B16Nid1 tumor 1, day 21
- GSM8371604 B16Nid1 tumor 2, day 21
- GSM8371605 B16Nid1 tumor 3, day 21
- GSM8371606 B16-Ats1KO tumor 1, day 21
- GSM8371607 B16-Ats1KO tumor 2, day 21
- GSM8371608 B16-Ats1KO tumor 3, day 21
- GSM8898341 B16F1 CD11b_cells 1
- GSM8898342 B16F1 CD11b_cells 2
- GSM8898343 B16F1 CD11b_cells 3
- GSM8898344 B16Nid1 CD11b_cells 1
- GSM8898345 B16Nid1 CD11b_cells 2
- GSM8898346 B16Nid1 CD11b_cells 3
- GSE263358 Chromatin Modification Abnormalities by CHD7 and KMT2C Loss Promote Medulloblastoma Progression [RNA-seq] 21 samples shares modification, progression
- GSE293383 Viscoelastic Extracellular Matrix Enhances Epigenetic Remodeling and Cellular Plasticity [RNA-seq] 12 samples shares extracellular, genetic
- GSE263362 Chromatin Modification Abnormalities by CHD7 and KMT2C Loss Promote Medulloblastoma Progression 71 samples shares modification, progression
- GSE241850 Psychological stress-induced ALKBH5 deficiency promotes tumour innervation and pancreatic cancer progression via extracellular vesicle transfer of m6A-modified RNAs 57 samples shares extracellular, progression
- GSE235109 Ensembles of genome-coverage single-cell histone modifications reveal epigenetic lineages during mouse preimplantation development 47 samples shares modification, genetic
- GSE263360 Chromatin Modification Abnormalities by CHD7 and KMT2C Loss Promote Medulloblastoma Progression [CUT&Tag] 36 samples shares modification, progression
- GSE259393 Ensembles of genome-coverage single-cell histone modifications reveal epigenetic lineages during mouse preimplantation development II 27 samples shares modification, genetic
- GSE308116 Epigenetic modification, as a distinctive therapeutic molecule for Parkinson’s disease gene therapy. 17 samples shares modification, genetic
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.