RNA-Seq based transcriptome analysis of colorectal cancer cells in response to lactate treatment
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 × SW480_NC vs 3 × SW480_LA vs 3 × DLD1_NC vs 3 × DLD1_LAGroups 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 GSE180948_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 PRJNA750094 and SRA study SRP330082. 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.
- GSM5479123 SW480_NC_1 SW480_NC
- GSM5479125 SW480_NC_2 SW480_NC
- GSM5479127 SW480_NC_3 SW480_NC
- GSM5479129 SW480_LA_1 SW480_LA
- GSM5479130 SW480_LA_2 SW480_LA
- GSM5479132 SW480_LA_3 SW480_LA
- GSM5479134 DLD1_NC_1 DLD1_NC
- GSM5479135 DLD1_NC_2 DLD1_NC
- GSM5479137 DLD1_NC_3 DLD1_NC
- GSM5479139 DLD1_LA_1 DLD1_LA
- GSM5479140 DLD1_LA_3 DLD1_LA
- GSM5479142 DLD1_LA_2 DLD1_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, rna-seq
- 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
- GSE109308 Single-cell transcriptomic survey of adenomatous polyposis patients with germline APC mutations 97 samples same disease briefing
- GSE292858 RNA-Seq analysis of tumor and matched normal samples from colorectal cancer patients. 73 samples shares colorectal, 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 treatment, rna-seq
- GSE294300 Single-cell gene expression profiles of cells from primary colorectal cancer and adjacent normal tissue [scRNA-Seq] 36 samples shares colorectal, rna-seq
- GSE318490 Single-cell RNA-seq of tumor samples from six advanced HGSOC patients across treatment stages (pre-NACT, post-NACT and platinum-sensitive recurrence) 10 samples shares treatment, 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.