BCR and TLR-induced IRF1 promotes T cell independent B cell responses by supporting Notch2 dependent Marginal Zone B cell development
RNA-seq (gene expression) · mouse · 24 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
- 24 samples: 24 samples, each with a distinct title — no replicated groupsGroups 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
- The Marginal Zone B Cell Compartment and T Cell-independent Antibody Responses Are Supported by B Cell Intrinsic Expression of IRF1Journal of immunology (Baltimore, Md. : 1950) · 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 GSE248790_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 PRJNA1046020 and SRA study SRP474785. Searching any of these in the dataset finder brings you back here.
Any grouping that defines a comparison lives in the sample characteristics, which GEO records separately from the titles.
How we read this: Read from 24 sample titles: 24 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.
- GSM7920120 EXP1_REPLICATE_1_WT.Trans.1.01
- GSM7920121 EXP1_REPLICATE_1_WT.Trans.2.01
- GSM7920122 EXP1_REPLICATE_1_WT.FoB.01
- GSM7920123 EXP1_REPLICATE_1_WT.MZB.01
- GSM7920124 EXP1_REPLICATE_2_WT.Trans.1.02
- GSM7920125 EXP1_REPLICATE_2_WT.Trans.2.02
- GSM7920126 EXP1_REPLICATE_2_WT.FoB.02
- GSM7920127 EXP1_REPLICATE_2_WT.MZB.02
- GSM7920128 EXP1_REPLICATE_3_WT.Trans.1.03
- GSM7920129 EXP1_REPLICATE_3_WT.Trans.2.03
- GSM7920130 EXP1_REPLICATE_3_WT.FoB.03
- GSM7920131 EXP1_REPLICATE_3_WT.MZB.03
- GSM7920132 EXP1_REPLICATE_1_IRF1.KO.Trans.1.01
- GSM7920133 EXP1_REPLICATE_1_IRF1.KO.Trans.2.01
- GSM7920134 EXP1_REPLICATE_1_IRF1.KO.FoB.01
- GSM7920135 EXP1_REPLICATE_1_IRF1.KO.MZB.01
- GSM7920136 EXP1_REPLICATE_2_IRF1.KO.Trans.1.02
- GSM7920137 EXP1_REPLICATE_2_IRF1.KO.Trans.2.02
- GSM7920138 EXP1_REPLICATE_2_IRF1.KO.FoB.02
- GSM7920139 EXP1_REPLICATE_2_IRF1.KO.MZB.02
- GSM7920140 EXP1_REPLICATE_3_IRF1.KO.Trans.1.03
- GSM7920141 EXP1_REPLICATE_3_IRF1.KO.Trans.2.03
- GSM7920142 EXP1_REPLICATE_3_IRF1.KO.FoB.03
- GSM7920143 EXP1_REPLICATE_3_IRF1.KO.MZB.03
- GSE274989 Identification of Myc-dependent and -independent Notch2 signatures in marginal zone B cells. 32 samples shares notch2, independent, dependent
- GSE335245 Forced Notch2 signaling instructs TLR and BCR responsiveness in B cells [RNA-Seq] 45 samples shares notch2, bcr
- GSE274992 Splenic fibroblasts control marginal zone B-cell movement and function via two distinct Notch2-dependent regulatory programs 119 samples shares notch2, dependent
- GSE297361 Loss of NOTCH2 Creates a TRIM28-Dependent Vulnerability in Small Cell Lung Cancer [bulk_murine_RNA_seq] 36 samples shares notch2, dependent
- GSE274990 Marginal zone B cells receive robust Notch2 signals within the B cell follicle in the absense of S1pr1 signaling. 42 samples shares notch2
- GSE300949 The murine meninges is a resilient B cell lymphopoietic reservoir conferring protection against infections [BCR-seq] 24 samples shares bcr
- GSE261822 Investigating Immune Escape of Chronic Myeloid Leukemia in Blast Crisis by Comparing T cells from miR-142 KO BCR-ABL versus miR-142 WT BCR-ABL mice 24 samples shares bcr
- GSE284008 RNA-sequencing data from mouse kidneys to identify candidate players in kidneys responding to VNS and/or macrophage-specific deletion of Notch2. 18 samples shares notch2
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.