Next Generation Sequencing Facilitates Quantitative Analysis of transcriptome and epigenome in skeletal stem cell sorted from Ptipfl/fl and Ptipf/f;Col2-Cre mice
ChIP-seq / ATAC-seq (genome binding and open chromatin) · mouse · 48 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
- 48 samples: 22 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
- Ptip safeguards the epigenetic control of skeletal stem cell quiescence and potency in skeletogenesisScience bulletin · 2024
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 GSE183543_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 PRJNA761208 and SRA study SRP335921. Searching any of these in the dataset finder brings you back here.
Supports a between-group comparison across 44 samples.
How we read this: 22 replicated groups read from 48 sample titles; they account for 44 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.
- GSM5560138 SSC-WT rep1 SSC-WT
- GSM5560139 SSC-WT rep2 SSC-WT
- GSM5560140 pBCSP-WT rep1 pBCSP-WT
- GSM5560141 pBCSP-WT rep2 pBCSP-WT
- GSM5560142 BCSP-WT rep1 BCSP-WT
- GSM5560143 BCSP-WT rep2 BCSP-WT
- GSM5560144 SSC Ptip-KO-rep1 SSC Ptip-KO
- GSM5560145 SSC Ptip-KO-rep2 SSC Ptip-KO
- GSM5560146 pBCSP-Ptip-KO-rep1 pBCSP-Ptip-KO
- GSM5560147 pBCSP-Ptip-KO-rep2 pBCSP-Ptip-KO
- GSM5560148 BCSP-Ptip-KO-rep1 BCSP-Ptip-KO
- GSM5560149 BCSP-Ptip-KO-rep2 BCSP-Ptip-KO
- GSM5560150 SSC-WT-H3K4me1 SSC-WT-H3K4me
- GSM5560151 SSC-WT-H3K4me3 SSC-WT-H3K4me
- GSM5560152 SSC-WT-H3K27ac SSC-WT-H3K27ac
- GSM5560153 SSC-WT-input-DNA SSC-WT-input-DNA
- GSM5560154 pBCSP-WT-H3K4me1 pBCSP-WT-H3K4me
- GSM5560155 pBCSP-WT-H3K4me3 pBCSP-WT-H3K4me
- GSM5560156 pBCSP-WT-H3K27ac
- GSM5560157 pBCSP-WT-input-DNA pBCSP-WT-input-DNA
- GSM5560158 BCSP-WT-H3K4me1 BCSP-WT-H3K4me
- GSM5560159 BCSP-WT-H3K4me3 BCSP-WT-H3K4me
- GSM5560160 BCSP-WT-H3K27ac BCSP-WT-H3K27ac
- GSM5560161 BCSP-WT-input-DNA BCSP-WT-input-DNA
- GSM5560162 SSC-KO-H3K4me1 SSC-KO-H3K4me
- GSM5560163 SSC-KO-H3K4me3 SSC-KO-H3K4me
- GSM5560164 SSC-KO-H3K27ac SSC-KO-H3K27ac
- GSM5560165 SSC-KO-input-DNA SSC-KO-input-DNA
- GSM5560166 pBCSP-KO-H3K4me1 pBCSP-KO-H3K4me
- GSM5560167 pBCSP-KO-H3K4me3 pBCSP-KO-H3K4me
- GSM5560168 pBCSP-KO-H3K27ac pBCSP-KO-H3K27ac
- GSM5560169 pBCSP-KO-input-DNA
- GSM5560170 BCSP-KO-H3K4me1 BCSP-KO-H3K4me
- GSM5560171 BCSP-KO-H3K4me3 BCSP-KO-H3K4me
- GSM5560172 BCSP-KO-H3K27ac BCSP-KO-H3K27ac
- GSM5560173 BCSP-KO-input-DNA BCSP-KO-input-DNA
- GSM5903580 SSC-WT-H3K27ac-rep2 SSC-WT-H3K27ac
- GSM5903581 SSC-WT-input-DNA-rep2 SSC-WT-input-DNA
- GSM5903582 PBCSP-WT-H3K27ac-rep2
- GSM5903583 pBCSP-WT-input-DNA-rep2 pBCSP-WT-input-DNA
+ 8 more — browse all 48 samples with per-sample file links →
- GSE248916 Metabolic Promotion of Adult and Aging Skeletal Muscle Regeneration by the Serine Biosynthesis Pathway 30 samples shares generation, skeletal
- GSE329069 Deletion of P311 enhances regeneration in aged skeletal muscle 9 samples shares generation, skeletal
- GSE255887 HDAC1 controls the generation and maintenance of effector-like CD8+ T cells during chronic viral infection 76 samples shares generation
- GSE222745 Enhanced activities of OCT4 and SOX2 facilitates epigenetic reprogramming by modulating cell cycle [scRNA-Seq] 422 samples shares facilitates
- GSE267938 Functional optic tract rewiring via subtype- and target-specific axonal regeneration and presynaptic activity enhancement 256 samples shares generation
- GSE240797 The microbiota and T cells non-genetically modulate inherited phenotypes transgenerationally 208 samples shares generation
- GSE272452 Generation of germinal-vesicle oocytes from mouse embryonic stem cells under an ovarian soma-free condition 202 samples shares generation
- GSE272353 Genetic context modulates aging and degeneration in the murine retina 201 samples shares generation
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.