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Sample GSM5060334 Query DataSets for GSM5060334
Status Public on Sep 15, 2021
Title Control
Sample type SRA
 
Source name ES cells
Organism Mus musculus
Characteristics treatment: wide-type
Growth protocol Mouse ES cells were cultured on 0.1% gelatin-coated plates with MEF feeder cells in LIF/2i media for 2 days.
Extracted molecule genomic DNA
Extraction protocol 50,000 cells were harvested and lysed in 50 μl of cold lysis buffer (10 mM Tris-HCl (pH 7.4), 10 mM NaCl, 3 mM MgCl2, 0.1% (v/v) Igepal CA-630) for 10 min on ice to prepare the nuclei. Then, spin down immediately at 500 g for 5 min, 4 °C, to remove the supernatant. Nuclei were then incubated with TruePrep Tagment Enzyme (TD501, Vazyme) at 55 °C for 10 min. Immediately after the tag mentation, 1× VAHTS DNA Clean Beads (N411, Vazyme) was added into the reaction to purify DNA fragments.
Nuclei were then incubated with TruePrep Tagment Enzyme (TD501, Vazyme) at 55 °C for 10 min. Immediately after the tag mentation, 1× VAHTS DNA Clean Beads (N411, Vazyme) was added into the reaction to purify DNA fragments. PCR amplify the library with the following program: 72 °C for 3 min; 98 °C for 30 s; and thermocycling at 1 cycle of 98 °C for 15 s, 15 cycles of 60 °C for 30 s and 72 °C for 3 min; following by 72 °C for 5 min. Libraries were purified with the 0.6×/0.15× double sided size selection. Libraries were sequenced with the Illumina HiSeq 2500 System.
 
Library strategy ATAC-seq
Library source genomic
Library selection other
Instrument model Illumina HiSeq 2500
 
Data processing Basecalls performed using CASAVA version 1.8
All bulk RNA-seq reads were trimmed using Trimmomatic software with the following parameters “ILLUMINACLIP:TruSeq3-PE.fa:2:30:10 LEADING:3 TRAILING:3 SLIDINGWINDOW:4:15 MINLEN:36” (Version 0.36). and were further quality-filtered using FASTX Toolkit’s fastq_quality_trimmer command (Version 0.0.13, http://hannonlab.cshl.edu/fastx_toolkit/) with the minimum quality score 20 and minimum percent of 80% bases that has a quality score larger than this cutoff value.
ATAC-seq reads were first aligned to mm10 genomes using Bowtie2 (version 2.3.4.1). The ATAC-seq reads were aligned with the parameters: -t -q -N 1 -L 25 -X 2000 no-mixed no-discordant.
The bamCoverage and bamCompare commands contained in deepTools (version 2.5.3) were adopted for downstream analysis. Using BamCoverage command with the parameters: -normalizeUsing BPM -of bigwig -binSize 100, we first normalized the raw reads signal to Bins Per Million mapped reads (BPM) signal and converted the alignment bam files to bigwig signal files. The bigwig files were imported into UCSC genome browser for visualization.
Genome_build: mm10
Supplementary_files_format_and_content: wig files were generated using deepTools
 
Submission date Feb 02, 2021
Last update date Sep 15, 2021
Contact name Hua Yu
E-mail(s) huayu@zju.edu.cn
Phone 18758008246
Organization name Zhejiang University
Street address 866 Yuhangtang Rd
City Hangzhou
ZIP/Postal code 310058
Country China
 
Platform ID GPL17021
Series (2)
GSE166022 rRNA Biogenesis Regulates Mouse 2C-like State by 3D Structure Reorganization of Peri-Nucleolar Heterochromatin [ATAC-seq]
GSE166041 rRNA Biogenesis Regulates Mouse 2C-like State by 3D Structure Reorganization of Peri-Nucleolar Heterochromatin
Relations
BioSample SAMN17764234
SRA SRX10008271

Supplementary file Size Download File type/resource
GSM5060334_ATACseq_Control.bw 88.5 Mb (ftp)(http) BW
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file

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