GEO series

Next-generation sequencing Facilitates Quantitative Analysis of Wild Type and EED-/- mice cerebellum Transcriptomes and Genome-wide maps of chromatin state in Wild Type and EED-/- mice cerebellum

GSE169312 Mus musculus (mouse) ChIP-seq / ATAC-seq (genome binding and open chromatin) 12 samples Submitted 2024/04/02 Platform GPL17021

At a glance

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: 12 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.

Summary (written by the submitters)

Purpose: The goals of this study are to compare Wild Type and EED-/- cerebellum transcriptome profiling (RNA-seq) to quantitative reverse transcription polymerase chain reaction (qRT–PCR) differentially expressed genes and find target genes. We performed chromatin-immunoprecipitation coupled to sequencing (ChIP-seq) to dissect the relationship between the differentially expressed genes and the occupancy of H3K27me3, H3K27ac and EED.

Read the full summary ↓

Methods: Cerebellum mRNA profiles of 14-day-old(P14) wild-type (WT) and Embryonic Ectoderm Development conditional knockout (EED-/-) mice were generated by deep sequencing, in triplicate,using Illumina HiSeq 2500 system.All RNA-Seq data were aligned to mouse genome version mm10 using Salmon (v.1.1.0) .We use cluster software and Euclidean distance matrix for the hierarchical clustering analysis of the expressed gene and sample program at the same time, the clustering results can be viewed with javaTreeview. qRT–PCR validation was performed using SYBR Green assays. we performed ChIP-seq using freshly isolated P14 from Wild Type and EED-/- cerebellar tissues . DNA libraries generated from ChIP-DNA and input-DNA were deep-sequenced using HiSeq single-end 50bp. Results:Only transcripts that showed more than 1.5-fold differential expression compared to control were subjected to relevance network analysis. 3149 candidate genes that were differentially expressed with biological functional groups as compared between WT and EED-/- mice .We found that the enrichment of H3K27me3 was decreased H3K27ac was highly increased in EED-/- mice. Conclusions: Our study represents the first detailed analysis of Wild Type and EED-/ mice cerebellum transcriptomes, with three biologic replicates, generated by RNA-seq technology. We report the application of ChIP-sequencing technology for high-throughput profiling of histone modifications in cerebellar cells.

This dataset

Open GSE169312 in finder → Find more mouse RNA-seq datasets →

Download · which file do I need?

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.

1 · Just have a look

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.

Series matrix ↓

2 · Re-analyse it

Supplementary files

The count tables and other files the authors uploaded. Take only the samples you need, or the whole study as GSE169312_RAW.tar (it can run to tens of gigabytes).

All supplementary files ↗ Whole study · RAW.tar ↓

3 · Start from the raw reads

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.

Raw reads on ENA ↗

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 PRJNA716253 and SRA study SRP311618. Searching any of these in the dataset finder brings you back here.

NCBI GEO page ↗

Study design

12 samples, each with a distinct title — no replicated groups

Any grouping that defines a comparison lives in the sample characteristics, which GEO records separately from the titles.

How we read this: Read from 12 sample titles: 12 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.

Samples in this study

GSM5195446 WT1 (RNA-seq)
GSM5195447 WT2 (RNA-seq)
GSM5195448 WT3 (RNA-seq)
GSM5195449 cKO1 (RNA-seq)
GSM5195450 cKO2 (RNA-seq)
GSM5195451 cKO3 (RNA-seq)
GSM5195452 WT_H3K27ac (ChIP-seq)
GSM5195453 WT_H3K27me3 (ChIP-seq)
GSM5195454 cKO_H3K27ac (ChIP-seq)
GSM5195455 cKO_H3K27me3 (ChIP-seq)
GSM5195456 WT_input (ChIP-seq)
GSM5195457 cKO_input (ChIP-seq)

Datasets on a similar topic

GSE278201 Next Generation Sequencing Facilitates Quantitative Analysis of BALB/C mice triple-negative breast cancer Transcriptomes 10 samples shares transcriptomes, quantitative, facilitates
GSE166226 Inference of emergent spatio-temporal processes from single-cell sequencing reveals feedback between de novo DNA methylation and chromatin condensates 615 samples shares eed, chromatin
GSE166225 Inference of emergent spatio-temporal processes from single-cell sequencing reveals feedback between de novo DNA methylation and chromatin condensates [RNA-seq] 288 samples shares eed, chromatin
GSE284165 Reorganization of PBAF/cBAF remodelers on H3.3 chromatin regulates BMAL1 activity in the absence of circadian negative feedback 47 samples shares eed, chromatin
GSE253581 Transcriptional profiling of CD11b+ microglia isolated from cerebellum and olfactory bulb-removed brains of K18-seeded P301L, PBS-injected P301L and PBS-injected FVB at 1-week, 1-month, and 3-months post-injection. 27 samples shares eed, cerebellum
GSE183543 Next Generation Sequencing Facilitates Quantitative Analysis of transcriptome and epigenome in skeletal stem cell sorted from Ptipfl/fl and Ptipf/f;Col2-Cre mice 48 samples shares quantitative, facilitates
GSE240160 Next Generation Sequencing Facilitates Quantitative Analysis of wild type and Rbm25-deficient Bone Marrow Derived macrophages 12 samples shares quantitative, facilitates
GSE168110 Next generation sequencing facilliates quantitative analysis of Wild type and KitW/Wv Smooth muscle cells transcriptomes 10 samples shares transcriptomes, quantitative

Search all mouse RNA-seq datasets in GEO →

Share this dataset

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.