Epigenetic and transcriptional regulation of dendritic cell development and anti-tumor function by HDAC1
ChIP-seq / ATAC-seq (genome binding and open chromatin) · mouse · 34 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
- 34 samples: 10 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
- The histone deacetylase HDAC1 controls dendritic cell development and anti-tumor immunityCell reports · 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 GSE266584_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 PRJNA1107623 and SRA study SRP505588. Searching any of these in the dataset finder brings you back here.
Supports a between-group comparison across 23 samples.
How we read this: 10 replicated groups read from 34 sample titles; they account for 23 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.
- GSM8252019 ATAC_cDC1_WT_1 ATAC_cDC1_WT
- GSM8252020 ATAC_cDC2 WT_1 ATAC_cDC2 WT
- GSM8252021 ATAC_cDC1_KO_1 ATAC_cDC1_KO
- GSM8252022 ATAC_cDC2 KO_1 ATAC_cDC2 KO
- GSM8252023 ATAC_cDC1_WT_2 ATAC_cDC1_WT
- GSM8252024 ATAC_cDC2 WT_2 ATAC_cDC2 WT
- GSM8252025 ATAC_cDC1_KO_2 ATAC_cDC1_KO
- GSM8252026 ATAC_cDC2 KO_2 ATAC_cDC2 KO
- GSM8252027 cDC2-KO1-H3K27ac
- GSM8252028 cDC2-KO1-IgG
- GSM8252029 cDC2-KO2-H3K27Ac
- GSM8252030 cDC2-KO2-IgG
- GSM8252031 cDC2-WT1-H3k27Ac
- GSM8252032 cDC2-WT1-IgG
- GSM8252033 cDC2-WT2-H3K27Ac
- GSM8252034 cDC2-WT2-IgG
- GSM8252035 cDC1_WT_1 cDC1_WT
- GSM8252036 cDC2 WT_1 cDC2 WT
- GSM8252037 pDC WT_1 pDC WT
- GSM8252038 cDC1_WT_2 cDC1_WT
- GSM8252039 cDC2 WT_2 cDC2 WT
- GSM8252040 pDC WT_2 pDC WT
- GSM8252041 cDC1_WT_3 cDC1_WT
- GSM8252042 pDC_WT_3
- GSM8252043 cDC2_WT_3
- GSM8252044 cDC1_KO_1 cDC1_KO
- GSM8252045 cDC2 KO_1 cDC2 KO
- GSM8252046 pDC KO_1 pDC KO
- GSM8252047 cDC1_KO_2 cDC1_KO
- GSM8252048 cDC2 KO_2 cDC2 KO
- GSM8252049 pDC KO_2 pDC KO
- GSM8252050 cDC1_KO_3 cDC1_KO
- GSM8252051 cDC2_KO_3
- GSM8252052 pDC KO_3 pDC KO
- GSE275917 Nup153 regulates neuronal responsiveness through HDAC1-mediated epigenetic modulation [ChIP-seq] 17 samples shares hdac1, epigenetic
- GSE300014 The CARM1 Epigenetic Enzyme Inhibits Cross-presenting Dendritic Cell Function in Cancer Immunity [RNA-seq] 26 samples shares epigenetic, dendritic
- GSE300019 The CARM1 Epigenetic Enzyme Inhibits Cross-presenting Dendritic Cell Function in Cancer Immunity [multiome] 8 samples shares epigenetic, dendritic
- GSE325195 Dendritic cell redundancy enables priming of anti-tumor CD4 T cells in pancreatic cancer 30 samples shares anti-tumor, dendritic
- GSE245838 Anchored screening identifies transcription factor blueprints underlying dendritic cell diversity and subset-specific anti-tumor immunity [mouse scRNA-seq] 21 samples shares anti-tumor, dendritic
- GSE255887 HDAC1 controls the generation and maintenance of effector-like CD8+ T cells during chronic viral infection 76 samples shares hdac1
- GSE272888 Dynamic transcriptional and epigenetic changes define postnatal tendon growth 54 samples shares epigenetic
- GSE157232 The CD8+ T cell tolerance checkpoint triggers a transcriptionally and epigenetically distinct differentiation state defined by protein translation defects 30 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.