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Sample GSM5514085 Query DataSets for GSM5514085
Status Public on Sep 15, 2021
Title TRIM28_Control_Input
Sample type SRA
Source name ES cells
Organism Mus musculus
Characteristics cell type: ES cells
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 2x10^6 cells were cross-linked for 10 min with 1% final concentration fresh formaldehyde and quenched by 0.2M glycine for 5 min. Lysates were clarified from sonicated nuclei and histone-DNA complexes were isolated with antibody.
Libraries were prepared according to VAHTS Universal DNA Library Prep Kit for Illumina V3 Kit (vazyme, ND607-01). Briefly, input DNA was phosphorylated at 5’ ends and dATP to yield a protruding 3-'A' base. After adapter ligation DNA was PCR amplified with Illumina primers for 15 cycles and library fragments of ~250 bp were purified by using DNA Clean Beads. Libraries were sequenced on the Illumina HiSeq 2500 following the manufacturer's protocols.
Library strategy ChIP-Seq
Library source genomic
Library selection ChIP
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, with the minimum quality score 20 and minimum percent of 80% bases that has a quality score larger than this cutoff value.
The ChIP-seq reads were aligned to mm10 with the options: -t -q -N 1 -L 25. All unmapped reads and PCR duplicates were removed.
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. To minimize the effect of chromatin structure and sequencing bias in our H3K9me3 ChIP-seq data, we corrected ChIP-seq signal using log2 ratio transformation between H3K9me3 signal and input signal by BamCompare command.
The “computeMatrix” and “plotProfile” commands of deepTools were used to produce the reads density distribution plot of ATAC-seq and ChIP-seq signal in the given genomic region.
Genome_build: mm10
Supplementary_files_format_and_content: wig files were generated using deepTools
Submission date Aug 11, 2021
Last update date Sep 15, 2021
Contact name Hua Yu
Phone 18758008246
Organization name Zhejiang University
Street address 866 Yuhangtang Rd
City Hangzhou
ZIP/Postal code 310058
Country China
Platform ID GPL17021
Series (2)
GSE166023 rRNA Biogenesis Regulates Mouse 2C-like State by 3D Structure Reorganization of Peri-Nucleolar Heterochromatin [ChIP-seq]
GSE166041 rRNA Biogenesis Regulates Mouse 2C-like State by 3D Structure Reorganization of Peri-Nucleolar Heterochromatin
BioSample SAMN20712893
SRA SRX11719202

Supplementary data files not provided
SRA Run SelectorHelp
Processed data provided as supplementary file
Raw data are available in SRA

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