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Sample GSM8496572 Query DataSets for GSM8496572
Status Public on Sep 18, 2024
Title Mouse, Naïve, E15.5, CDYL antibody, Rep1
Sample type SRA
 
Source name Mouse cortex
Organism Mus musculus
Characteristics tissue: Mouse cortex
cell line: NA
cell type: whole cortex
genotype: naive
chip antibody: CDYL (Proteintech, 17763-1-AP)
time: E15.5
Extracted molecule genomic DNA
Extraction protocol ChIP DNA degradation and contamination was monitored on agarose gels. DNA purity was checked using the NanoPhotometer® spectrophotometer (IMPLEN, CA, USA). DNA concentration was measured using Qubit® DNA Assay Kit in Qubit® 3.0 Flurometer (Life Technologies, CA, USA).
The purified DNA was used for ChIP-seq library preparation. The library was constructed by Novogene Corporation (Beijing, China). Subsequently, pair-end sequencing of sample was performed on Illumina platform (Illumina, CA, USA). Library quality was assessed on the Agilent Bioanalyzer 2100 system.
 
Library strategy ChIP-Seq
Library source genomic
Library selection ChIP
Instrument model Illumina NovaSeq 6000
 
Data processing Raw data (raw reads) of fastq format were firstly processed using fastp (version 0.19.11, Chen et al., 2018) software. In this step, clean data (clean reads) were obtained by removing reads containing adapter, reads containing ploy-N and low quality reads from raw data. At the same time, Q20, Q30 and GC content of the clean data were calculated. All the downstream analyses were based on the clean data with high quality.
Reference genome and gene model annotation files were downloaded from genome website directly. Bowtie 2 were used to align the raw data with the reference genome. The SAM file generated from Bowtie2 was then converted to a BAM file using SAMtools. Next, we generated coverage files in the BigWig (.bw) format for visualization in genome browsers such as IGV or UCSC Genome Browser. This was accomplished using bedtools and deepTools.
Assembly: hg18 & mm19
Supplementary files format and content: .bw
 
Submission date Sep 04, 2024
Last update date Sep 18, 2024
Contact name Liang-Yu Ni
E-mail(s) nly123@pku.edu.cn
Phone 18075062311
Organization name Peking University
Street address Peking university Health Science center
City Beijing
State/province Beijing
ZIP/Postal code 100083
Country China
 
Platform ID GPL24247
Series (1)
GSE276321 Chromodomain protein CDYL confers forebrain identity to human cortical organoids by inhibiting neuronatin [ChIP-seq]
Relations
BioSample SAMN43496486
SRA SRX25968101

Supplementary file Size Download File type/resource
GSM8496572_Mouse_CDYL_Rep1.bw 75.5 Mb (ftp)(http) BW
SRA Run SelectorHelp
Raw data are available in SRA

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