Comprehensive transcriptome characterization deciphers mechanisms underpinning the positive selection of B cells in germinal centers. [mouse; short-read]
RNA-seq (gene expression) · mouse · 20 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
- 20 samples: 5 × Mouse naïve short-read vs 5 × Mouse DZ short-read vs 5 × Mouse LZ GFP-cMYCneg short-read vs 5 × Mouse LZ GFP-cMYCpos short-readGroups 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 GSE278742_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 PRJNA1168549 and SRA study SRP536447. Searching any of these in the dataset finder brings you back here.
Supports a between-group comparison across 20 samples.
How we read this: 4 replicated groups read from 20 sample titles; they account for 20 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.
- GSM8554006 Mouse naïve short-read rep1 Mouse naïve short-read
- GSM8554007 Mouse naïve short-read rep2 Mouse naïve short-read
- GSM8554008 Mouse naïve short-read rep3 Mouse naïve short-read
- GSM8554009 Mouse naïve short-read rep4 Mouse naïve short-read
- GSM8554010 Mouse naïve short-read rep5 Mouse naïve short-read
- GSM8554011 Mouse DZ short-read rep1 Mouse DZ short-read
- GSM8554012 Mouse DZ short-read rep2 Mouse DZ short-read
- GSM8554013 Mouse DZ short-read rep3 Mouse DZ short-read
- GSM8554014 Mouse DZ short-read rep4 Mouse DZ short-read
- GSM8554015 Mouse DZ short-read rep5 Mouse DZ short-read
- GSM8554016 Mouse LZ GFP-cMYCneg short-read rep1 Mouse LZ GFP-cMYCneg sh…
- GSM8554017 Mouse LZ GFP-cMYCneg short-read rep2 Mouse LZ GFP-cMYCneg sh…
- GSM8554018 Mouse LZ GFP-cMYCneg short-read rep3 Mouse LZ GFP-cMYCneg sh…
- GSM8554019 Mouse LZ GFP-cMYCneg short-read rep4 Mouse LZ GFP-cMYCneg sh…
- GSM8554020 Mouse LZ GFP-cMYCneg short-read rep5 Mouse LZ GFP-cMYCneg sh…
- GSM8554021 Mouse LZ GFP-cMYCpos short-read rep1 Mouse LZ GFP-cMYCpos sh…
- GSM8554022 Mouse LZ GFP-cMYCpos short-read rep2 Mouse LZ GFP-cMYCpos sh…
- GSM8554023 Mouse LZ GFP-cMYCpos short-read rep3 Mouse LZ GFP-cMYCpos sh…
- GSM8554024 Mouse LZ GFP-cMYCpos short-read rep4 Mouse LZ GFP-cMYCpos sh…
- GSM8554025 Mouse LZ GFP-cMYCpos short-read rep5 Mouse LZ GFP-cMYCpos sh…
- GSE237128 Myc transcriptional bursts promote B cell positive selection by T cells in germinal centers 16 samples shares selection, positive, germinal, centers
- GSE333139 Siglec-G on B cells restrains the germinal center response by controlling T cell help during positive selection 3 samples shares selection, positive, germinal
- GSE269197 Cathepsin L-Dependent Positive Selection Shapes Clonal Composition and Functional Fitness of CD4 T Cells [RNA] 13 samples shares selection, positive
- GSE319325 Proteasome alteration between epithelial and hematopoietic cells facilitates positive selection of CD8 T cells 6 samples shares selection, positive
- GSE244802 Csk restrains BCR-mediated ROS production and contributes to germinal center selection and affinity maturation 5 samples shares selection, germinal
- GSE271698 B cell-intrinsic IFN-g promotes CD11c+ age-associated B cell differentiation and compromises affinity-based germinal center selection in lupus 1 samples shares selection, germinal
- GSE313769 SATB1 Lowers The TCR Signaling Threshold For Thymocytes Positive Selection via Super-enhancer Reprogramming 122 samples shares selection, positive
- GSE330985 Positive and Negative Selection of abT cells (OT-I and OT-II) in the thymus 2 - scRNA-seq, CITE-seq and TCRab 21 samples shares selection, positive
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.