The PLAGL1-KLF4-IRX5 axis promotes the osteogenesis of periosteal progenitors during mandible regeneration [CUT＆tag-Seq]
ChIP-seq / ATAC-seq (genome binding and open chromatin) · mouse · 9 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
- 9 samples: 9 samples, each with a distinct title — no replicated groupsGroups 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 GSE298229_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 PRJNA1268544 and SRA study SRP587956. Searching any of these in the dataset finder brings you back here.
Any grouping that defines a comparison lives in the sample characteristics, which GEO records separately from the titles.
How we read this: Read from 9 sample titles: 9 distinct titles with little repetition. 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.
- GSM9010141 PLAGL1_HA_CUTtagseq
- GSM9010142 PLAGL1_igG_CUTtagseq
- GSM9010143 H3K4me3_CUTtagseq
- GSM9010144 KLF4_FLAG_Control_rep1_CUTtagseq
- GSM9010145 KLF4_FLAG_Control_rep2_CUTtagseq
- GSM9010146 KLF4_FLAG_Control_rep3_CUTtagseq
- GSM9010147 KLF4_FLAG_Plagl1ko_rep1_CUTtagseq
- GSM9010148 KLF4_FLAG_Plagl1ko_rep2_CUTtagseq
- GSM9010149 KLF4_FLAG_Plagl1ko_rep3_CUTtagseq
- GSE279042 Reprogramming of epidermal keratinocytes by PITX1 transforms the cutaneous cellular landscape and promotes wound healing [CUT&Tag] 30 samples shares cut, promotes
- GSE275296 H3K36 methylation regulates cell plasticity and regeneration in the intestinal epithelium [cutandtag_enzyme_profiling] 12 samples shares cut, regeneration
- GSE280862 Loss of Sarm1 Mitigates Axonal Degeneration and Promotes Neuronal Regeneration After Ischemic Stroke 15 samples shares regeneration, promotes
- GSE272702 Topical lubrication restores dry eye corneal stroma by producing reparative keratocytesacripep promotes corneal regeneration in autoimmune mediated dry eye disease. 12 samples shares regeneration, promotes
- GSE304211 H4K16ac contributes to chromatin compartment reorganization during mitotic and meiotic transitions [CUTnTAG] 128 samples shares cut
- GSE297309 SKP1A-mediated degradation of PRC2 triggers activation of Polycomb-silenced gene [CUT&Tag] 108 samples shares cut
- GSE289642 Noncanonical PRC2 chromatin association reveals a key role of EZHIP in intergenerational epigenetic memory transition [ChIP-Seq, Cut & Run] 107 samples shares cut
- GSE303384 Mechanism of maintenance and establishment of repression by the Mtg16 tumor suppressor [CUT&RUN, ChIP-Seq] 92 samples shares cut
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.