Degradation of Ikaros prevents epigenetic progression of T cell exhaustion in novel antigen-specific assay
ChIP-seq / ATAC-seq (genome binding and open chromatin) · human · 15 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
- 15 samples: 6 × TT_bulkATAC_untreated vs 5 × TT_bulkATAC_iberdomide vs 2 × ATAC_DonorPool vs 2 × RNA_DonorPoolGroups 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.
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 GSE244184_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 PRJNA1021613 and SRA study SRP463527. Searching any of these in the dataset finder brings you back here.
Supports a between-group comparison across 15 samples.
How we read this: 4 replicated groups read from 15 sample titles; they account for 15 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.
- GSM7808000 ATAC_DonorPool_1 ATAC_DonorPool
- GSM7808001 ATAC_DonorPool_2 ATAC_DonorPool
- GSM7808365 RNA_DonorPool_1 RNA_DonorPool
- GSM7808366 RNA_DonorPool_2 RNA_DonorPool
- GSM7808373 TT_bulkATAC_untreated_rep1 TT_bulkATAC_untreated
- GSM7808374 TT_bulkATAC_untreated_rep2 TT_bulkATAC_untreated
- GSM7808375 TT_bulkATAC_untreated_rep3 TT_bulkATAC_untreated
- GSM7808376 TT_bulkATAC_untreated_rep4 TT_bulkATAC_untreated
- GSM7808377 TT_bulkATAC_untreated_rep5 TT_bulkATAC_untreated
- GSM7808378 TT_bulkATAC_untreated_rep6 TT_bulkATAC_untreated
- GSM7808379 TT_bulkATAC_iberdomide_rep1 TT_bulkATAC_iberdomide
- GSM7808380 TT_bulkATAC_iberdomide_rep2 TT_bulkATAC_iberdomide
- GSM7808381 TT_bulkATAC_iberdomide_rep3 TT_bulkATAC_iberdomide
- GSM7808382 TT_bulkATAC_iberdomide_rep4 TT_bulkATAC_iberdomide
- GSM7808383 TT_bulkATAC_iberdomide_rep5 TT_bulkATAC_iberdomide
- GSE301719 Mezigdomide reverses T cell exhaustion through degradation of Aiolos/Ikaros and reinvigoration of cytokine production pathways 74 samples shares degradation, exhaustion, ikaros
- GSE304097 DNA methylation profiling identifies long-range epigenetic silencing of clustered protocadherins as a key determinant of meningioma progression 293 samples shares progression, epigenetic
- GSE270787 ZIC2 and ZIC3 promote SWI/SNF recruitment to safeguard progression towards human primed pluripotency 205 samples shares progression
- 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
- GSE243526 Defining the Regulatory Logic of Breast Cancer Using Single-Cell Epigenetic and Transcriptome Profiling 40 samples shares epigenetic
- GSE324206 Spatially-Resolved Multiomic Atlas of Leiomyosarcoma Identifies Two Clinically Relevant Epigenetically-Driven Cell States [scMultiomic] 32 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.