Genetic and epigenetic screens in primary human T cells link candidate causal autoimmune variants to T cell networks
RNA-seq (gene expression) · human · 21 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
- 21 samples: 7 × Primary T MPRA mRNA vs 5 × MPRA plasmidGroups 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 GSE297472_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 PRJNA1264797 and SRA study SRP583802. Searching any of these in the dataset finder brings you back here.
Supports a between-group comparison across 12 samples.
How we read this: 2 replicated groups read from 21 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.
- GSM8973681 01_G1104_t0
- GSM8973682 02_G1104_pro
- GSM8973683 11_G1121_t0
- GSM8973684 12_G1121_pro
- GSM8973685 21_G1130_t0
- GSM8973686 22_G1130_pro
- GSM8973687 31_H1130_t0
- GSM8973688 32_H1130_pro
- GSM8992651 Primary T MPRA mRNA rep 1 Primary T MPRA mRNA
- GSM8992652 Primary T MPRA mRNA rep 2 Primary T MPRA mRNA
- GSM8992653 Primary T MPRA mRNA rep 3 Primary T MPRA mRNA
- GSM8992654 Primary T MPRA mRNA rep 4 Primary T MPRA mRNA
- GSM8992655 Primary T MPRA mRNA rep 5 Primary T MPRA mRNA
- GSM8992656 Primary T MPRA mRNA rep 6 Primary T MPRA mRNA
- GSM8992657 Primary T MPRA mRNA rep 7 Primary T MPRA mRNA
- GSM8992658 MPRA plasmid rep 1 MPRA plasmid
- GSM8992659 MPRA plasmid rep 2 MPRA plasmid
- GSM8992660 MPRA plasmid rep 3 MPRA plasmid
- GSM8992661 MPRA plasmid rep 4 MPRA plasmid
- GSM8992662 MPRA plasmid rep 5 MPRA plasmid
- GSM8992663 Oligo/barcode pairings
- GSE297471 Genetic and epigenetic screens in primary human T cells link candidate causal autoimmune variants to T cell networks [MPRA] 13 samples shares epigenetic, autoimmune, candidate, variants, networks, genetic, screens, primary
- GSE306915 Integrated epigenetic and genetic programming of primary human T cells [RNA-seq] 77 samples shares epigenetic, genetic, primary
- GSE293136 Multimodal remodeling of epigenetic and enhancer networks shapes the transcriptional landscape of beige adipocytes 66 samples shares epigenetic, networks, genetic
- GSE290517 Epigenetic priming of embryonic enhancer elements coordinates developmental gene networks [CUT&TAG] 45 samples shares epigenetic, networks, genetic
- GSE277909 Epigenetic attenuation of interferon signaling drives aging-related improvements in systemic lupus 271 samples shares epigenetic, genetic
- GSE234181 Long-term multi-modal recording reveals epigenetic adaptation routes in dormant breast cancer cells [scRNA-Seq] 184 samples shares epigenetic, genetic
- GSE232076 In vitro reconstitution of epigenetic reprogramming in the human germ line [RNA-Seq] 89 samples shares epigenetic, genetic
- GSE311877 Genotype-phenotype single-cell transcriptomics for massive parallel assessment of genetic variants [RNAseq_mutants] 80 samples shares variants, genetic
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.