Inhibition of DEK contributes to the tolerance of replication stress and restores HSC function in Fanconi anemia [12-ATAC]
ChIP-seq / ATAC-seq (genome binding and open chromatin) · human · 10 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
- 10 samples: 5 × ATAC_FA vs 5 × ATAC_HealthyGroups 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 GSE281513_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 PRJNA1184169 and SRA study SRP544244. Searching any of these in the dataset finder brings you back here.
Supports a between-group comparison across 10 samples.
How we read this: 2 replicated groups read from 10 sample titles; they account for 10 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.
- GSM8622330 ATAC_FA_1 ATAC_FA
- GSM8622331 ATAC_FA_2 ATAC_FA
- GSM8622332 ATAC_FA_3 ATAC_FA
- GSM8622333 ATAC_FA_4 ATAC_FA
- GSM8622334 ATAC_FA_5 ATAC_FA
- GSM8622335 ATAC_Healthy_1 ATAC_Healthy
- GSM8622336 ATAC_Healthy_2 ATAC_Healthy
- GSM8622337 ATAC_Healthy_3 ATAC_Healthy
- GSM8622338 ATAC_Healthy_4 ATAC_Healthy
- GSM8622339 ATAC_Healthy_5 ATAC_Healthy
- GSE263299 Mis-splicing of mitotic regulators sensitizes SF3B1-mutated human HSCs to CHK1 inhibition [RNA-seq] 10 samples shares hsc, inhibition
- GSE242205 Intrahepatic immune microenvironment contributes to spontaneous tolerance in pediatric liver transplantation recipients 18 samples shares contributes, tolerance
- GSE293213 A viral circular RNA in Kaposi’s sarcoma-associated herpesvirus contributes to viral and host gene expression during latent and lytic replication 10 samples shares contributes, replication
- GSE324916 Phosphorylation of serines 287/288 in DEK regulates cell-type-specific chromatin occupancy and compaction [ChIP-Seq] 24 samples shares dek
- GSE326270 Phosphorylation of serines 287/288 in DEK regulates cell-type-specific chromatin occupancy and compaction [ATAC-seq] 12 samples shares dek
- GSE329274 Phosphorylated DEK sustains leukemia stem cells by enabling PBX3-driven transcriptional reprogramming [CUT&Tag 2] 12 samples shares dek
- GSE307624 ATACSeq of TET2-mutant human HSCs 11 samples shares hsc
- GSE316079 SLF2 and SMC5 dysfunction drives HSC aging and predisposes to MDS, defining a new inherited bone marrow failure syndrome [ATAC-seq] 6 samples shares hsc
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.