Genome-wide discovery and integrative genomic characterization of insulin resistance loci using serum triglycerides to HDL-cholesterol ratio [bulk RNA-seq]
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)
- Samples
- 12 samples: 3 × SGBS_Day0 vs 3 × SGBS_Day4 vs 3 × SGBS_Day8 vs 3 × SGBS_Day15Groups 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
- Genome-wide discovery and integrative genomic characterization of insulin resistance loci using serum triglycerides to HDL-cholesterol ratio as a proxyNature communications · 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 GSE274839_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 PRJNA1148159 and SRA study SRP526403. 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.
- GSM8458895 SGBS_Day0_Replicate1 SGBS_Day0
- GSM8458896 SGBS_Day4_Replicate1 SGBS_Day4
- GSM8458897 SGBS_Day8_Replicate1 SGBS_Day8
- GSM8458898 SGBS_Day15_Replicate1 SGBS_Day15
- GSM8458899 SGBS_Day0_Replicate2 SGBS_Day0
- GSM8458900 SGBS_Day4_Replicate2 SGBS_Day4
- GSM8458901 SGBS_Day8_Replicate2 SGBS_Day8
- GSM8458902 SGBS_Day15_Replicate2 SGBS_Day15
- GSM8458903 SGBS_Day0_Replicate3 SGBS_Day0
- GSM8458904 SGBS_Day4_Replicate3 SGBS_Day4
- GSM8458905 SGBS_Day8_Replicate3 SGBS_Day8
- GSM8458906 SGBS_Day15_Replicate3 SGBS_Day15
- GSE281303 Multimodal Genome-wide Survey of Progressing and Non-progressing Breast Ductal Carcinoma In-Situ [RNA-seq] 123 samples shares genome-wide, rna-seq
- GSE273829 GABA promotes resistance to immunotherapy of patients with TLS-positive tumors [RNA-seq] 92 samples shares resistance, rna-seq
- GSE245948 A dynamic subcutaneous adipose transcriptome of human insulin resistance identifies a molecular predisposition shared with visceral adipose tissue 76 samples shares resistance, insulin
- GSE293952 Hypoxia shapes both therapeutic response and resistance in metastatic clear cell renal cell carcinoma [bulk RNA-seq] 61 samples shares resistance, rna-seq
- GSE268092 TFE3 fusion proteins drive oxidative metabolism, ferroptosis resistance and general RNA synthesis in translocation renal cell carcinoma. [RNA-seq] 36 samples shares resistance, rna-seq
- GSE304579 Alternative End-Joining Activation by miR-21-5p Confers Radiation Resistance in Oral Squamous Cell Carcinoma [RNA-seq of SUGH-OSCC patient tumors] 34 samples shares resistance, rna-seq
- GSE303100 Dissecting Resistance to CDK4/6 Inhibition in Experimental Glioma via Genome-wide CRISPR-Cas9 Screening 24 samples shares genome-wide, resistance
- GSE326661 Reprogramming engineered autologous T cells to overcome resistance in Merkel cell carcinoma [scRNA-seq] 22 samples shares resistance, 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.