TRMT6-mediated tRNA m1A modification acts as a translational checkpoint of histone synthesis and facilitates colorectal cancer progression
Non-coding RNA profiling · human · 18 samples
- What it is
- Non-coding RNA profilingLevels of RNAs that do not code for proteins, such as miRNA or lncRNA.
- 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.
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 GSE233361_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.
Also filed as BioProject PRJNA975919 and SRA study SRP439400. 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.
- GSM7426223 tRNA ShControl rep 1 tRNA ShControl
- GSM7426224 tRNA ShControl rep 2 tRNA ShControl
- GSM7426225 tRNA ShControl rep 3 tRNA ShControl
- GSM7426226 tRNA ShTRMT6 rep 1 tRNA ShTRMT6
- GSM7426227 tRNA ShTRMT6 rep 2 tRNA ShTRMT6
- GSM7426228 tRNA ShTRMT6 rep 3 tRNA ShTRMT6
- GSM7426249 RNA ShControl rep 1 RNA ShControl
- GSM7426250 RNA ShControl rep 2 RNA ShControl
- GSM7426251 RNA ShControl rep 3 RNA ShControl
- GSM7426252 RNA ShTRMT6 rep 1 RNA ShTRMT6
- GSM7426253 RNA ShTRMT6 rep 2 RNA ShTRMT6
- GSM7426254 RNA ShTRMT6 rep 3 RNA ShTRMT6
- GSM7426257 Ribo ShControl rep 1 Ribo ShControl
- GSM7426258 Ribo ShControl rep 2 Ribo ShControl
- GSM7426259 Ribo ShControl rep 3 Ribo ShControl
- GSM7426260 Ribo ShTRMT6 rep 1 Ribo ShTRMT6
- GSM7426261 Ribo ShTRMT6 rep 2 Ribo ShTRMT6
- GSM7426262 Ribo ShTRMT6 rep 3 Ribo ShTRMT6
- GSE12032 Inherent gene signature of stage II and III colorectal cancer leads in individual recurrence 198 samples same disease briefing · shares colorectal
- 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
- 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
- GSE256353 Upregulated cholesterol biosynthesis facilitates the survival of methylation-retaining AML cells following decitabine treatment [single_colony_TEM-Seq] 1728 samples shares facilitates, synthesis
- GSE271703 Integrated ChIP-seq and Transcriptomic Profiling of Histone Modifications Across Breast Cancer Progression in MCF10A-Derived Cell Lines [ChIP-Seq] 60 samples shares modification, progression
- GSE284582 Pan-modification profiling facilitates a cross-evolutionary dissection of the thermoregulated ribosomal epitranscriptome - Hsapi 34 samples shares modification, facilitates
- GSE264114 An Improved SNAP-ADAR Tool Enables Efficient RNA Base Editing to Interfere with Post-translational Protein Modification 26 samples shares translational, modification
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.