Transcriptomic Diversity of Innate Lymphoid Cells in Human Lymph nodes
Single-cell RNA-seq · human · 14 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
- 14 samples: 4 × BM vs 4 × Spl vs 3 × LN abdominal vs 3 × LN thoracicGroups 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
- Transcriptomic diversity of innate lymphoid cells in human lymph nodes compared to BM and spleenCommunications biology · 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 GSE243033_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 PRJNA1016253 and SRA study SRP460156. Searching any of these in the dataset finder brings you back here.
Supports a between-group comparison across 14 samples.
How we read this: 4 replicated groups read from 14 sample titles; they account for 14 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.
- GSM7777732 LN abdominal replicate 1 LN abdominal
- GSM7777733 LN abdominal replicate 2 LN abdominal
- GSM7777734 LN abdominal replicate 3 LN abdominal
- GSM7777735 LN thoracic replicate 1 LN thoracic
- GSM7777736 LN thoracic replicate 2 LN thoracic
- GSM7777737 LN thoracic replicate 3 LN thoracic
- GSM7777738 BM replicate 1 BM
- GSM7777739 BM replicate 2 BM
- GSM7777740 BM replicate 3 BM
- GSM7777741 BM replicate 4 BM
- GSM7777742 Spl replicate 1 Spl
- GSM7777743 Spl replicate 2 Spl
- GSM7777744 Spl replicate 3 Spl
- GSM7777745 Spl replicate 4 Spl
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- GSE286234 Bulk RNA-seq profiling of human head and neck squamous cell carcinoma (HNSCC) with primary tumors and metastatic lymph nodes 10 samples shares lymph, nodes
- GSE272410 Molecular and spatial analysis unveils the functional basis of tertiary lymphoid structures in Sjogren’s syndrome[bulk RNA-seq] 73 samples shares lymphoid, lymph
- GSE306950 Dysregulated NK Cell Activation and Myeloid-Lymphoid Imbalance Underpin COPD Progression: Insights from High-Dimensional Immune Profiling and Smoking-Induced Immune Remodeling 35 samples shares lymphoid, lymph
- GSE248214 Breast cancer remodels lymphatics in sentinel lymph nodes 22 samples shares lymph, nodes
- GSE277742 Immune Landscape of Intrathoracic Lymph Nodes with Metastasis in Primary Lung Malignancy using EBUS-TBNA samples 22 samples shares lymph, nodes
- GSE272346 Late-stage tertiary lymphoid structures in hepatocellular carcinoma treated with neoadjuvant immune checkpoint blockade [bulk RNA-seq] 14 samples shares lymphoid, lymph
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.