Effect of depletion of C15ORF48/miR-147 on gene expression in primary colonocytes
RNA-seq (gene expression) · human · 24 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)
- Samples
- 24 samples: 20 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
- The epithelial C15ORF48/miR-147-NDUFA4 axis is an essential regulator of gut inflammation, energy metabolism, and the microbiomeProceedings of the National Academy of Sciences of the United States of America · 2024
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 GSE246494_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 PRJNA1033337 and SRA study SRP468998. Searching any of these in the dataset finder brings you back here.
How we read this: Read from 24 sample titles: 20 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.
- GSM7869797 WT1
- GSM7869798 WT2
- GSM7869799 WT3
- GSM7869800 WT1-DSS
- GSM7869801 WT2-DSS
- GSM7869802 WT3-DSS
- GSM7869803 KO2
- GSM7869804 KO4
- GSM7869805 KO5
- GSM7869806 KO1-DSS
- GSM7869807 KO2-DSS
- GSM7869808 KO3-DSS
- GSM7869809 47616_PCW-1
- GSM7869810 47617_PCW-2
- GSM7869811 47618_PCW-IL1b-1
- GSM7869812 47619_PCW-IL1b-2
- GSM7869813 47620_83-1
- GSM7869814 47621_83-2
- GSM7869815 47622_83-IL1b-1
- GSM7869816 47623_83-IL1b-2
- GSM7869817 47624_A2
- GSM7869818 47625_A2-IL1b
- GSM7869819 47626_B2
- GSM7869820 47627_B2-IL1b
- GSE172333 A myeloid maturation program initiated by nucleotide depletion during S phase [RNA-Seq] 158 samples shares depletion
- GSE297591 Cytotoxicity caused by 5-methylcytosine depletion on chromatin-associated RNA by 5-azacytosine in leukemia [RNA-seq] 96 samples shares depletion
- GSE260966 Selective depletion of HBV-infected hepatocytes by class A capsid assembly modulators require high levels of intrahepatic HBV core protein 76 samples shares depletion
- GSE172299 A myeloid maturation program initiated by nucleotide depletion during S phase [ATAC-Seq] 48 samples shares depletion
- GSE297589 Cytotoxicity caused by 5-methylcytosine depletion on chromatin-associated RNA by 5-azacytosine in leukemia [CUT&Tag] 38 samples shares depletion
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.