Induction of a transcriptional adaptation response by RNA destabilization events [dst175]
ChIP-seq / ATAC-seq (genome binding and open chromatin) · mouse · 12 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
- 12 samples: 3 × Wildtype vs 3 × PTC1 vs 3 × PTC2 vs 3 × LDGroups 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 GSE286097_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 PRJNA1207915 and SRA study SRP555998. Searching any of these in the dataset finder brings you back here.
Supports a between-group comparison across 12 samples.
How we read this: 4 replicated groups read from 12 sample titles; they account for 12 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.
- GSM8717704 Wildtype_1 Wildtype
- GSM8717705 Wildtype_2 Wildtype
- GSM8717706 Wildtype_3 Wildtype
- GSM8717707 PTC1_1 PTC1
- GSM8717708 PTC1_2 PTC1
- GSM8717709 PTC1_3 PTC1
- GSM8717710 PTC2_1 PTC2
- GSM8717711 PTC2_2 PTC2
- GSM8717712 PTC2_3 PTC2
- GSM8717713 LD_1 LD
- GSM8717714 LD_2 LD
- GSM8717715 LD_3 LD
- GSE245647 The Heme-regulated transcriptional repressor, BACH1 safeguards macrophage enhancer selection, activation andtissue adaptation [ChIP-seq] 62 samples shares adaptation
- GSE245646 The Heme-regulated transcriptional repressor, BACH1 safeguards macrophage enhancer selection, activation andtissue adaptation [ATAC-seq_muscle] 22 samples shares adaptation
- GSE245645 The Heme-regulated transcriptional repressor, BACH1 safeguards macrophage enhancer selection, activation andtissue adaptation [ATAC-seq_BMDM] 12 samples shares adaptation
- GSE301998 IL-25-induced effector-memory ILC2s mediate small intestinal adaptation [ATAC-seq] 36 samples shares adaptation
- GSE165460 Induction of senescence upon loss of the Ash2l subunit of histone H3K4 methyltransferase complexes (ChIP-Seq) 20 samples shares induction
- GSE241770 ACSS2 mediates an epigenetic pathway to regulate maternal Beta-cell adaptation and progression of gestational diabetes (scRNA-Seq) 7899 samples shares adaptation
- GSE274144 ATAC-seq of VLDLR+ vs VLDLR- HSCs after acute anemia induction 14 samples shares induction
- GSE283255 Distinct Vps34-orchestrated signaling processes dictate the transitional heterogeneity and functional adaptation of effector Treg cells [ATAC-seq2] 14 samples shares adaptation
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.