Small intestinal lymph node identity is defined by medullary stromal cells in humans and mice [Sorted_lns_macrophages_RNAseq]
RNA-seq (gene expression) · mouse · 45 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
- Mus musculus (mouse)
- Samples
- 45 samples: 15 conditions, mostly in triplicateGroups 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.
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 GSE282129_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 PRJNA1187251. Searching any of these in the dataset finder brings you back here.
Supports a between-group comparison across 45 samples.
How we read this: 15 replicated groups read from 45 sample titles; they account for 45 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.
- GSM8636516 Duodenal LN SCM_1 Duodenal LN SCM
- GSM8636517 Duodenal LN SCM_2 Duodenal LN SCM
- GSM8636518 Duodenal LN SCM_3 Duodenal LN SCM
- GSM8636519 Jejunal LN SCM_1 Jejunal LN SCM
- GSM8636520 Jejunal LN SCM_2 Jejunal LN SCM
- GSM8636521 Jejunal LN SCM_3 Jejunal LN SCM
- GSM8636522 Ileal LN SCM_1 Ileal LN SCM
- GSM8636523 Ileal LN SCM_2 Ileal LN SCM
- GSM8636524 Ileal LN SCM_3 Ileal LN SCM
- GSM8636525 Ceco-colonic LN SCM_1 Ceco-colonic LN SCM
- GSM8636526 Ceco-colonic LN SCM_2 Ceco-colonic LN SCM
- GSM8636527 Ceco-colonic LN SCM_3 Ceco-colonic LN SCM
- GSM8636528 Inguinal LN SCM_1 Inguinal LN SCM
- GSM8636529 Inguinal LN SCM_2 Inguinal LN SCM
- GSM8636530 Inguinal LN SCM_3 Inguinal LN SCM
- GSM8636531 Duodenal LN MCM_1 Duodenal LN MCM
- GSM8636532 Duodenal LN MCM_2 Duodenal LN MCM
- GSM8636533 Duodenal LN MCM_3 Duodenal LN MCM
- GSM8636534 Jejunal LN MCM_1 Jejunal LN MCM
- GSM8636535 Jejunal LN MCM_2 Jejunal LN MCM
- GSM8636536 Jejunal LN MCM_3 Jejunal LN MCM
- GSM8636537 Ileal LN MCM_1 Ileal LN MCM
- GSM8636538 Ileal LN MCM_2 Ileal LN MCM
- GSM8636539 Ileal LN MCM_3 Ileal LN MCM
- GSM8636540 Ceco-colonic LN MCM_1 Ceco-colonic LN MCM
- GSM8636541 Ceco-colonic LN MCM_2 Ceco-colonic LN MCM
- GSM8636542 Ceco-colonic LN MCM_3 Ceco-colonic LN MCM
- GSM8636543 Inguinal LN MCM_1 Inguinal LN MCM
- GSM8636544 Inguinal LN MCM_2 Inguinal LN MCM
- GSM8636545 Inguinal LN MCM_3 Inguinal LN MCM
- GSM8636546 Duodenal LN MSM_1 Duodenal LN MSM
- GSM8636547 Duodenal LN MSM_2 Duodenal LN MSM
- GSM8636548 Duodenal LN MSM_3 Duodenal LN MSM
- GSM8636549 Jejunal LN MSM_1 Jejunal LN MSM
- GSM8636550 Jejunal LN MSM_2 Jejunal LN MSM
- GSM8636551 Jejunal LN MSM_3 Jejunal LN MSM
- GSM8636552 Ileal LN MSM_1 Ileal LN MSM
- GSM8636553 Ileal LN MSM_2 Ileal LN MSM
- GSM8636554 Ileal LN MSM_3 Ileal LN MSM
- GSM8636555 Ceco-colonic LN MSM_1 Ceco-colonic LN MSM
+ 5 more — browse all 45 samples with per-sample file links →
- GSE319684 Timecourse of FACS sorted Ly6C+ monocytes, tissue resident alveolar macrophages (trAMs), monocyte derived alveolar macrophages (bmAMs) and epithelial cells from SARS-CoV-2 (maVie16) vs. IAV (PR8) infected mouse lungs 176 samples shares macrophages, sorted
- GSE300283 The single-cell transcriptome defines an effector Vd1 gd T cell-dependent anti-tumor immunity in human gastrointestinal stromal tumor (GIST) 6 samples shares intestinal, stromal
- GSE300757 Efferocytosis induces proangiogenic function and chromatin remodeling in tumor-associated macrophages 127 samples shares macrophages
- GSE319035 P21+TREM2+-Senescent Macrophages Fuel Inflammaging and Metabolic Dysfunction-Associated Steatotic Liver Disease [NAFLD_time_course] 77 samples shares macrophages
- GSE280514 Spatially-restricted and ontogenically-distinct hepatic macrophages are required for tissue repair. 48 samples shares macrophages
- GSE268774 Lymph node macrophages drive immune tolerance and resistance to cancer therapy by expression of the immune-regulatory cytokine IL-33 [RNA-seq] 48 samples shares macrophages
- GSE300925 Lyn expression in macrophages promotes TLR activation and restricts proliferation in an isoform-independent manner 48 samples shares macrophages
- GSE205410 Multiple subpopulations in medullary thymic epithelial cells are regulated by Aire with distinctive modes of gene regulations [bulkRNA-seq] 47 samples shares medullary
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.