SLAM-seq reveals the promotive role of NDRG1 in Fusobacterium nucleatum-induced Tumorigenesis in Colorectal Cancer.
RNA-seq (gene expression) · human · 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
- Homo sapiens (human)
- Topic
- Colorectal cancerThis series is part of our curated briefing on it.
- Samples
- 12 samples: 3 × HCT116 cells infected by Fn, 4sU labeling 2 hours, vs 3 × HCT116 cells infected by Fn, no 4sU labeling, vs 3 × HCT116 cells, 4sU labeling, vs 3 × HCT116 cells, no 4sU labeling,Groups 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 GSE297086_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 PRJNA1262492 and SRA study SRP585001. Searching any of these in the dataset finder brings you back here.
Supports a between-group comparison across 12 samples.
How we read this: 4 replicated groups read from 12 sample titles; they account for 12 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.
- GSM8983468 HCT116 cells infected by Fn, 4sU labeling 2 hours,rep1 HCT116 cells infected b…
- GSM8983469 HCT116 cells infected by Fn, 4sU labeling 2 hours,rep2 HCT116 cells infected b…
- GSM8983470 HCT116 cells infected by Fn, 4sU labeling 2 hours,rep3 HCT116 cells infected b…
- GSM8983471 HCT116 cells infected by Fn, no 4sU labeling,rep1 HCT116 cells infected b…
- GSM8983472 HCT116 cells infected by Fn, no 4sU labeling,rep2 HCT116 cells infected b…
- GSM8983473 HCT116 cells infected by Fn, no 4sU labeling,rep3 HCT116 cells infected b…
- GSM8983474 HCT116 cells, 4sU labeling,rep1 HCT116 cells, 4sU label…
- GSM8983475 HCT116 cells, 4sU labeling,rep2 HCT116 cells, 4sU label…
- GSM8983476 HCT116 cells, 4sU labeling,rep3 HCT116 cells, 4sU label…
- GSM8983477 HCT116 cells, no 4sU labeling,rep1 HCT116 cells, no 4sU la…
- GSM8983478 HCT116 cells, no 4sU labeling,rep2 HCT116 cells, no 4sU la…
- GSM8983479 HCT116 cells, no 4sU labeling,rep3 HCT116 cells, no 4sU la…
- 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
- GSE110009 Single cell transcriptome landscape of primary and metastatic tumor in colon cancer 76 samples same disease briefing
- GSE124480 Gene expression of human colon cancer HCT116 cells 5 samples same disease briefing
- GSE109308 Single-cell transcriptomic survey of adenomatous polyposis patients with germline APC mutations 97 samples same disease briefing
- GSE273567 Secretory IgA dysfunction underlies poor prognosis in Fusobacterium-infected colorectal cancer 42 samples shares fusobacterium, colorectal
- GSE247894 HMGA1 promotes the tumorigenesis of colorectal cancer by increasing lipid synthesis 6 samples shares tumorigenesis, colorectal
- GSE245617 The adhesin RadD enhances Fusobacterium nucleatum tumor colonization and colorectal carcinogenesis 9 samples shares fusobacterium, colorectal
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.