Bulk RNA seq of sorted CD11c cells from lungs of uninfected and Mtb infected wild type mice.
RNA-seq (gene expression) · mouse · 10 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
- 10 samples: 5 × Uninfected Zeb2 fl/fl vs 5 × Mtb infected Zeb2 fl/flGroups 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
- Nuclear Factor κB Signaling Deficiency in CD11c-Expressing Phagocytes Mediates Early Inflammatory Responses and Enhances Mycobacterium tuberculosis ControlThe Journal of infectious diseases · 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 GSE249963_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 PRJNA1051504 and SRA study SRP477505. Searching any of these in the dataset finder brings you back here.
Supports a between-group comparison across 10 samples.
How we read this: 2 replicated groups read from 10 sample titles; they account for 10 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.
- GSM7968194 Uninfected Zeb2 fl/fl rep1 Uninfected Zeb2 fl/fl
- GSM7968195 Uninfected Zeb2 fl/fl rep2 Uninfected Zeb2 fl/fl
- GSM7968196 Uninfected Zeb2 fl/fl rep3 Uninfected Zeb2 fl/fl
- GSM7968197 Uninfected Zeb2 fl/fl rep4 Uninfected Zeb2 fl/fl
- GSM7968198 Uninfected Zeb2 fl/fl rep5 Uninfected Zeb2 fl/fl
- GSM7968199 Mtb infected Zeb2 fl/fl rep1 Mtb infected Zeb2 fl/fl
- GSM7968200 Mtb infected Zeb2 fl/fl rep2 Mtb infected Zeb2 fl/fl
- GSM7968201 Mtb infected Zeb2 fl/fl rep3 Mtb infected Zeb2 fl/fl
- GSM7968202 Mtb infected Zeb2 fl/fl rep4 Mtb infected Zeb2 fl/fl
- GSM7968203 Mtb infected Zeb2 fl/fl rep5 Mtb infected Zeb2 fl/fl
- GSE249704 Transcriptional profiles of tumor-draining lymph node resident CD11c+ cells in wildtype versus APOE-KO mice 12 samples shares cd11c, wild, type
- 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 infected, sorted, lungs
- GSE263080 RNA-sea of Smad4 wild-type or Smad4 knockout KPC PDAC organoids from monocultures or co-cultures with pancreatic stellate cells and RNA-seq of flow-sorted PSCs from the same co-cultures. 44 samples shares sorted, wild, type
- GSE263081 RNA-sea of Smad4 wild-type or Smad4 knockout KvPC PDAC organoids from monocultures or co-cultures with pancreatic stellate cells and RNA-seq of flow-sorted PSCs from the same co-cultures. 35 samples shares sorted, wild, type
- GSE300035 Analyzing the impact of antibiotics treatment on lung inflammation in Mtb infected mouse lungs using bulk RNA transcriptomics 20 samples shares infected, lungs, bulk
- GSE262926 Micro bulk sequencing on murine Bleomycin-induced fibrotic lungs sorted on SA-β-Gal and GD3 15 samples shares sorted, lungs, bulk
- GSE280963 Comparison of transcriptional response in ZIKV-infected wildtype (B6J) and RIPK3 KO neurons 12 samples shares infected, wild, type
- GSE129746 RNA-seq data of Ly6Chigh CD11c+ MHC-II+ and Ly6C low cells FACS-sorted from Mock-LLC and SULT2B1b-LLC tumors 15 samples shares cd11c, sorted
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.