Divergent Epigenetic and Transcriptomic Remodelling during Monocyte Subset Differentiation in Systemic Lupus Erythematosus [RNA-seq]
Single-cell RNA-seq · human · 57 samples
- What it is
- Single-cell RNA-seqGene activity measured in thousands of individual cells, so cell types can be told apart. Read from the summary: GEO's own type field only says 'expression profiling by sequencing', so confirm it in the paper.
- Organism
- Homo sapiens (human)
- Samples
- 57 samples: 39 distinct titles, 3 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
- Disease activity drives divergent epigenetic and transcriptomic reprogramming of monocyte subpopulations in systemic lupus erythematosusAnnals of the rheumatic diseases · 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 GSE249619_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: Single-cell studies usually ship their counts as 10x files (matrix.mtx, barcodes.tsv, features.tsv), an .h5 file, or an .rds / .h5ad object that Seurat or Scanpy can open. Look for those among the supplementary files.
Also filed as BioProject PRJNA1049831 and SRA study SRP476492. Searching any of these in the dataset finder brings you back here.
How we read this: Read from 57 sample titles: 39 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.
- GSM7951853 ClassicalMonocytes_SLE_1_Visit1
- GSM7951854 IntermediateMonocytes_SLE_1_Visit1
- GSM7951855 NonClassicalMonocytes_SLE_1_Visit1
- GSM7951856 ClassicalMonocytes_SLE_2_Visit1
- GSM7951857 IntermediateMonocytes_SLE_2_Visit1
- GSM7951858 NonClassicalMonocytes_SLE_2_Visit1
- GSM7951859 ClassicalMonocytes_SLE_5_Visit1
- GSM7951860 IntermediateMonocytes_SLE_5_Visit1
- GSM7951861 NonClassicalMonocytes_SLE_5_Visit1
- GSM7951862 ClassicalMonocytes_SLE_6_Visit1
- GSM7951863 IntermediateMonocytes_SLE_6_Visit1
- GSM7951864 NonClassicalMonocytes_SLE_6_Visit1
- GSM7951865 ClassicalMonocytes_SLE_7_Visit1
- GSM7951866 IntermediateMonocytes_SLE_7_Visit1
- GSM7951867 NonClassicalMonocytes_SLE_7_Visit1
- GSM7951868 ClassicalMonocytes_SLE_8_Visit1
- GSM7951869 IntermediateMonocytes_SLE_8_Visit1
- GSM7951870 NonClassicalMonocytes_SLE₈_Visit1
- GSM7951871 ClassicalMonocytes_SLE_9_Visit1
- GSM7951872 IntermediateMonocytes_SLE_9_Visit1
- GSM7951873 NonClassicalMonocytes_SLE_9_Visit1
- GSM7951874 ClassicalMonocytes_SLE_13_Visit1
- GSM7951875 IntermediateMonocytes_SLE_13_Visit1
- GSM7951876 NonClassicalMonocytes_SLE_13_Visit1
- GSM7951877 ClassicalMonocytes_SLE_17_Visit1
- GSM7951878 IntermediateMonocytes_SLE_17_Visit1
- GSM7951879 NonClassicalMonocytes_SLE_17_Visit1
- GSM7951880 ClassicalMonocytes_SLE_19_Visit1
- GSM7951881 IntermediateMonocytes_SLE_19_Visit1
- GSM7951882 NonClassicalMonocytes_SLE_19_Visit1
- GSM7951883 ClassicalMonocytes_SLE_21_Visit1
- GSM7951884 IntermediateMonocytes_SLE_21_Visit1
- GSM7951885 NonClassicalMonocytes_SLE_21_Visit1
- GSM7951886 ClassicalMonocytes_SLE_22_Visit1
- GSM7951887 IntermediateMonocytes_SLE_22_Visit1
- GSM7951888 NonClassicalMonocytes_SLE_22_Visit1
- GSM7951889 ClassicalMonocytes_HealthyDonor_24
- GSM7951890 IntermediateMonocytes_HealthyDonor_24
- GSM7951891 NonClassicalMonocytes_HealthyDonor_24
- GSM7951892 ClassicalMonocytes_HealthyDonor_26
+ 17 more — browse all 57 samples with per-sample file links →
- GSE254176 Dynamic changes of immune cells in systemic lupus erythematosus with nephritis using longitudinal peripheral blood single-cell RNA-seq 57 samples shares erythematosus, systemic, rna-seq
- GSE277909 Epigenetic attenuation of interferon signaling drives aging-related improvements in systemic lupus 271 samples shares epigenetic, systemic
- GSE234181 Long-term multi-modal recording reveals epigenetic adaptation routes in dormant breast cancer cells [scRNA-Seq] 184 samples shares epigenetic, rna-seq
- GSE232076 In vitro reconstitution of epigenetic reprogramming in the human germ line [RNA-Seq] 89 samples shares epigenetic, rna-seq
- GSE306915 Integrated epigenetic and genetic programming of primary human T cells [RNA-seq] 77 samples shares epigenetic, rna-seq
- GSE190564 Divergent spatial microdomains drive inflammation and repair in Ulcerative and Immune Checkpoint Therapy Colitis - whole tissue scRNA-Seq 62 samples shares divergent, rna-seq
- GSE282444 Epigenetic Memory of Intestinal Epithelial Cells in Inflammatory Bowel Disease [RNA-seq] 56 samples shares epigenetic, rna-seq
- GSE270505 Epigenetic heterogeneity and state-specific transcriptional programs determine differential drug response in osteosarcoma [RNA-seq] 19 samples shares epigenetic, 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.