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Sample GSM7431425 Query DataSets for GSM7431425
Status Public on May 29, 2023
Title NSC_siSCR_Chd4_ChIP_Seq
Sample type SRA
 
Source name Brain
Organism Mus musculus
Characteristics tissue: Brain
cell type: primary neural stem cell
genotype: wild type
treatment: growth medium
Growth protocol Cortical mouse NPCs were cultured using P0 mouse cortex in laminin and poly-L-ornithine-coated plates and maintained in DMEM/F12 (11320033, Thermo) containing 1% penicillin/streptomycin, 1% l-glutamine, 1% N-2 supplement, 1% B27,1×Glutamax (10565-042, Life technologies),5 mM Hepes, 0.06% Glucose, 50 μM beta-mercaptoethanol, 20 ng/ml EGFand 20 ng/ml bFGF
Extracted molecule genomic DNA
Extraction protocol Cells were fixed with 1% formaldehyde for 10 minutes. After quenching and cell lysis, chromatin was sonicated using a M220 focused-ultrasonicator (Covaris).
ChIP-seq libraries were prepared using the KAPA HyperPrep Kits (Roche, 07962347001) following manufacturer's protocols..
 
Library strategy ChIP-Seq
Library source genomic
Library selection ChIP
Instrument model Illumina NovaSeq 6000
 
Data processing The image analysis and base calling were performed by using Illumina’s Genome Analysis pipeline.
The sequencing reads were aligned to the human genome UCSC build hg18 by using Bowtie2 alignment programs in two ways: only uniquely aligned reads were kept or both uniquely aligned reads and the sequencing reads that align to repetitive regions were kept for downstream analysis (if a read aligns to multiple genome locations, only one location is arbitrarily chosen).
The multiple reads were collapsed in order to reduce the PCR biases. The aligned reads were used for peak finding with HOMER
Peaks were identified by searching locations of high read density using a 200-bp sliding window. Regions of maximal density exceeding a given threshold were called as peaks, and we required adjacent peaks to be at least 500 bp away to avoid redundant detection
Peaks from separate experiments were considered equivalent/co-bound if their peak centers were located within 200 bp of each other. Read density heat maps were created by first using HOMER to generate read densities and then visualized using Java TreeView
Assembly: hg38
Supplementary files format and content: xls, bigWig (except for Input sample)
 
Submission date May 27, 2023
Last update date May 29, 2023
Contact name Ximing Nian
E-mail(s) nianximing@yeah.net
Phone 18759108482
Organization name Shanghai Jiao Tong University
Street address Chongqing Nanlu 227
City shanghai
State/province Shanghai
ZIP/Postal code 201600
Country China
 
Platform ID GPL24247
Series (1)
GSE233613 Deletion of nucleoporin Seh1 impaired neurogenesis through transcriptional regulation (ChIP-Seq)
Relations
BioSample SAMN35444573
SRA SRX20528680

Supplementary file Size Download File type/resource
GSM7431425_NSC_siSCR_Chd4_ChIP_Seq.bw 282.5 Mb (ftp)(http) BW
GSM7431425_NSC_siSCR_Chd4_ChIP_Seq.txt.gz 184.7 Kb (ftp)(http) TXT
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file

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