RNA-seq analysis of human healthy and osteoarthritis meniscus reveals autophagy-related mRNAs and long noncoding RNAs
RNA-seq (gene expression) · human · 10 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
- 10 samples: 5 × Meni_O vs 5 × Meni_YGroups 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
- Identifying autophagy-related mRNAs and potential ceRNA networks in meniscus degeneration based on RNA sequencing and experimental validationHeliyon · 2024
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 GSE263210_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 PRJNA1096285 and SRA study SRP499746. Searching any of these in the dataset finder brings you back here.
Supports a between-group comparison across 10 samples.
How we read this: 2 replicated groups read from 10 sample titles; they account for 10 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.
- GSM8187638 Meni_O_1 Meni_O
- GSM8187639 Meni_O_2 Meni_O
- GSM8187640 Meni_O_3 Meni_O
- GSM8187641 Meni_O_4 Meni_O
- GSM8187642 Meni_O_5 Meni_O
- GSM8187643 Meni_Y_1 Meni_Y
- GSM8187644 Meni_Y_2 Meni_Y
- GSM8187645 Meni_Y_3 Meni_Y
- GSM8187646 Meni_Y_4 Meni_Y
- GSM8187647 Meni_Y_5 Meni_Y
- GSE267412 Novel Long Noncoding RNA HEAT4 Affects Monocyte Subtypes, Reducing Inflammation and Promoting Vascular Healing [RNA-seq_KD] 14 samples shares noncoding, rna-seq, long
- GSE267644 Novel Long Noncoding RNA HEAT4 Affects Monocyte Subtypes, Reducing Inflammation and Promoting Vascular Healing [scRNA-seq HF] 11 samples shares noncoding, rna-seq, long
- GSE335366 hLMR1, a hepatocyte-specific long noncoding RNA that represses amino acid catabolism through pre-mRNA interaction in human liver [RNA-seq] 9 samples shares noncoding, rna-seq, long
- GSE288868 X-Linked Cancer-Associated Polypeptide, Encoded by a Putative Noncoding RNA, Regulates Gene Expression and Cellular Pathways in Breast Cancer [RNA-seq] 48 samples shares noncoding, rna-seq
- GSE283079 Bulk RNA-seq of human knee osteoarthritis synovium 41 samples shares osteoarthritis, rna-seq
- GSE293276 Synovial Dysregulation in Ankle Osteoarthritis: Molecular Insights and Pathogenetic Pathways [RNA-Seq 1] 34 samples shares osteoarthritis, rna-seq
- GSE256420 Long Noncoding VIM-AS1: Biomarker of Breast Fibrosis Susceptibility After Radiation Therapy and Promoter of Transforming Growth Factor Beta1–Driven Fibrosis 27 samples shares noncoding, long
- GSE284007 The long noncoding RNA C1QTNF1-AS1 interacts with RSRC2 to ensure mitotic fidelity 24 samples shares noncoding, long
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.