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Sample GSM6739172 Query DataSets for GSM6739172
Status Public on Nov 18, 2023
Title H3K27me3 inh rep2
Sample type SRA
 
Source name whole brain
Organism Mus musculus
Characteristics tissue: whole brain
cell type: inhibitory neuron
genotype: Sun1 f/f | Emx1Cre (+)
age: 8 weeks
chip antibody: H3K27me3
Growth protocol Mice were maintained and bred in a 12-hour light/dark cycle under standard pathogen-free conditions.
Extracted molecule genomic DNA
Extraction protocol Nuclei were isolated from adult mouse brain tissue and subjected to FACS-sorting. The FACS-sorted nuclei were used for Cut&Run with the CUTANA CUT&RUN Kit. The Cut&Run enriched DNA fragments were used for DNA library construction.
Cut&Run libraries were prepared using the NEBNext Ultra II DNA Library Prep Kit for Illumina (NEB) following the manufacturer's instructions.
 
Library strategy OTHER
Library source genomic
Library selection other
Instrument model Illumina NovaSeq 6000
 
Data processing Sequencing adapters and low-quality bases were first trimed with cutadapt(v1.18) and trim_galore(v0.5.0) for all cun&run libraries. The retained reads were aligned to mouse genome(mm10) using bowtie2(v2.3.5) in pair-end mode with option “-N 1 -L 25”.
PCR duplications were removed using picard(v2.25.0) with the option “REMOVE_DUPLICATES=true”. Non-redundant reads were further filtered for minimal mapping quality (MAPQ ≥ 30) using samtools(v1.12) view with option “-q30”.
Peak calling for histone modifications was performed by MACS2(v2.2.5) using option “-p 0.05” for H3K27ac and H3K4me3, “--broad -p 0.05” for H3K4me1 and H3K27me3. The reproducible peaks between biological replicates was further identified following irreproducible discovery rate (IDR, v2.0.4.2) framework with parameters “--rank signal.value”.
Stricter parameters were adopted for EGR1 cun&run datasets peak calling to generate the reliable transcription factor binding sites,with option “-p 0.005” for MACS2 and “--rank signal.value --idr-threshold 0.02” for IDR framework.
Assembly: mm10
Supplementary files format and content: narrowPeak, broad Peak
Library strategy: Cut&Run
 
Submission date Nov 18, 2022
Last update date Nov 18, 2023
Contact name Xiguang Xu
E-mail(s) xiguang@vt.edu
Organization name Virginia Tech
Department Department of Biomedical Sciences and Pathobiology
Lab Epigenomics and Computational Biology Laboratory
Street address 1015 Life Science Circle
City Blacksburg
State/province VA
ZIP/Postal code 24060
Country USA
 
Platform ID GPL24247
Series (1)
GSE218312 Histone modifications mediate transcription factor regulation and contribute to neuronal subtype identity
Relations
BioSample SAMN31785149
SRA SRX18306235

Supplementary file Size Download File type/resource
GSM6739172_H3K27me3-in-r2_peaks.broadPeak.gz 5.1 Mb (ftp)(http) BROADPEAK
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file

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