B cell differentiation into germinal center and antibody-secreting cells depends on SMARCA5-mediated chromatin remodeling
ChIP-seq / ATAC-seq (genome binding and open chromatin) · mouse · 31 samples
- What it is
- ChIP-seq / ATAC-seq (genome binding and open chromatin)Where proteins bind the genome, or which regions are open and active.
- Organism
- Mus musculus (mouse)
- Samples
- 31 samples: 8 conditions, mostly with about 4 replicates eachGroups 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
- SMARCA5-mediated chromatin remodeling is required for germinal center formationThe Journal of experimental medicine · 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 GSE261015_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: Look for peak files (.bed, .narrowPeak) and signal tracks (.bigWig) among the supplementary files; the raw reads are on ENA.
Also filed as BioProject PRJNA1084819 and SRA study SRP514765. Searching any of these in the dataset finder brings you back here.
Supports a between-group comparison across 29 samples.
How we read this: 8 replicated groups read from 31 sample titles; they account for 29 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.
- GSM8127389 Smarca5_1 Smarca5
- GSM8127390 Smarca5_2 Smarca5
- GSM8127391 isotype_1 isotype
- GSM8127392 isotype_2 isotype
- GSM8127393 Smar_Cntrl1 Smar_Cntrl
- GSM8127394 Smar_Cntrl2 Smar_Cntrl
- GSM8127395 Smar_Cntrl3 Smar_Cntrl
- GSM8127396 Smar_Cntrl4 Smar_Cntrl
- GSM8127397 Smar_Cntrl5 Smar_Cntrl
- GSM8127398 Smar_Cntrl6 Smar_Cntrl
- GSM8127399 Smar_KO1 Smar_KO
- GSM8127400 Smar_KO2 Smar_KO
- GSM8127401 Smar_KO3 Smar_KO
- GSM8132043 Smarca5_KO
- GSM8132044 Smarca5_cntrl
- GSM8336939 DZ_sort_1 DZ_sort
- GSM8336940 DZ_sort_2 DZ_sort
- GSM8336941 DZ_sort_3 DZ_sort
- GSM8336942 DZ_sort_4 DZ_sort
- GSM8336943 DZ_sort-IP_1 DZ_sort-IP
- GSM8336944 DZ_sort-IP_2 DZ_sort-IP
- GSM8336945 DZ_sort-IP_3 DZ_sort-IP
- GSM8336946 DZ_sort-IP_4 DZ_sort-IP
- GSM8336947 LZ_sort_1 LZ_sort
- GSM8336948 LZ_sort_2 LZ_sort
- GSM8336949 LZ_sort_3 LZ_sort
- GSM8336950 LZ_sort_4 LZ_sort
- GSM8336951 LZ_sort-IP_1 LZ_sort-IP
- GSM8336952 LZ_sort-IP_2 LZ_sort-IP
- GSM8336953 LZ_sort-IP_3 LZ_sort-IP
- GSM8336954 LZ_sort-IP_4 LZ_sort-IP
- GSE248369 The Swi/Snf chromatin remodeling complex regulates pancreatic endocrine cell expansion and differentiation in vivo 10 samples shares remodeling, chromatin
- GSE300757 Efferocytosis induces proangiogenic function and chromatin remodeling in tumor-associated macrophages 127 samples shares remodeling, chromatin
- GSE239470 Condensate-promoting ENL mutation induces tumorigenesis via chromatin remodeling 74 samples shares remodeling, chromatin
- GSE278100 Foxa1-Mediated Chromatin Remodeling and Enhancer Reprogramming Promotes Gemcitabine Resistance in Pancreatic Cancer 54 samples shares remodeling, chromatin
- GSE299114 Endothelial Cells retain inflammatory memory through chromatin remodeling [RNA-Seq 2] 53 samples shares remodeling, chromatin
- GSE274493 The remodeling of bivalent chromatin is essential for mouse peri-implantation embryogenesis [CUT&Tag] 46 samples shares remodeling, chromatin
- GSE301108 Stag2 dependent chromatin remodeling enforces the erythroid-specific Gata1 cistrome 45 samples shares remodeling, chromatin
- GSE320350 Nuclear class 3 PI3K co-activates fasting-specific chromatin remodeling 12 samples shares remodeling, chromatin
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.