|
|
GEO help: Mouse over screen elements for information. |
|
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 Selector |
Raw data are available in SRA |
|
|
|
|
|