BCG vaccination alters the epigenetic landscape of progenitor cells in human bone marrow to influence innate immune responses
ChIP-seq / ATAC-seq (genome binding and open chromatin) · human · 42 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
- Homo sapiens (human)
- Samples
- 42 samples: 15 conditions, mostly in duplicateGroups 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
- BCG vaccination alters the epigenetic landscape of progenitor cells in human bone marrow to influence innate immune responsesImmunity · 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 GSE248730_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 PRJNA1045664 and SRA study SRP474453. Searching any of these in the dataset finder brings you back here.
Supports a between-group comparison across 42 samples.
How we read this: 15 replicated groups read from 42 sample titles; they account for 42 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.
- GSM7919093 B1 B
- GSM7919094 B2 B
- GSM7919095 B3 B
- GSM7919096 B4 B
- GSM7919097 B5 B
- GSM7919098 B6 B
- GSM7919099 B7 B
- GSM7919100 B8 B
- GSM7919101 B9 B
- GSM7919102 B10 B
- GSM7919103 B11 B
- GSM7919104 B12 B
- GSM7919105 B13 B
- GSM7919106 B14 B
- GSM7919184 B1_c1 B1_c
- GSM7919185 B1_c2 B1_c
- GSM7919186 B2_c1 B2_c
- GSM7919187 B2_c2 B2_c
- GSM7919188 B3_c1 B3_c
- GSM7919189 B3_c2 B3_c
- GSM7919190 B4_c1 B4_c
- GSM7919191 B4_c2 B4_c
- GSM7919192 B5_c1 B5_c
- GSM7919193 B5_c2 B5_c
- GSM7919194 B6_c1 B6_c
- GSM7919195 B6_c2 B6_c
- GSM7919196 B7_c1 B7_c
- GSM7919197 B7_c2 B7_c
- GSM7919198 B8_c1 B8_c
- GSM7919199 B8_c2 B8_c
- GSM7919200 B9_c1 B9_c
- GSM7919201 B9_c2 B9_c
- GSM7919202 B10_c1 B10_c
- GSM7919203 B10_c2 B10_c
- GSM7919204 B11_c1 B11_c
- GSM7919205 B11_c2 B11_c
- GSM7919206 B12_c1 B12_c
- GSM7919207 B12_c2 B12_c
- GSM7919208 B13_c1 B13_c
- GSM7919209 B13_c2 B13_c
+ 2 more — browse all 42 samples with per-sample file links →
- GSE301133 Lung mucosal and systemic responses at single-cell resolution in an aerosolised Mycobacterium bovis BCG human challenge model 159 samples shares bcg
- GSE269877 Single-cell RNA-sequencing of BCG naïve and recurrent non-muscle invasive bladder cancer reveals a CD6/ALCAM-mediated immune-suppressive pathway 38 samples shares bcg
- GSE322495 Divergent Macrophage-Regulated T cell States Determine Response to Bacillus Calmette-Guérin (BCG) in High-Risk Bladder Cancer 21 samples shares bcg
- GSE262098 Transcriptomes during monocyte-to-macrophage differentiation and BCG induced trained immunity in vitro 21 samples shares bcg
- GSE270296 TGF-β Signaling Pathway and Cell-Cell Interactions in the Tumor Microenvironment Drive Bladder Cancer Progression after BCG Instillation Treatment: Insights from longitudinal Single-Nucleus RNA-Seq 14 samples shares bcg
- GSE254521 Epigenetic priming promotes acquisition of TKI resistance and oncogene amplification in human lung cancer 146 samples shares epigenetic
- GSE278576 Epigenetic and 3D genome reprogramming during the aging of human hippocampus 80 samples shares epigenetic
- GSE283621 Single-cell multi-omics analysis identifies metabolism-linked epigenetic reprogramming as a driver of therapy-resistant medulloblastoma 79 samples shares epigenetic
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.