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Status |
Public on May 29, 2023 |
Title |
NSC_siSCR_Chd4_ChIP_Seq |
Sample type |
SRA |
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Source name |
Brain
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Organism |
Mus musculus |
Characteristics |
tissue: Brain cell type: primary neural stem cell genotype: wild type treatment: growth medium
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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
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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..
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Library strategy |
ChIP-Seq |
Library source |
genomic |
Library selection |
ChIP |
Instrument model |
Illumina NovaSeq 6000 |
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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)
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Submission date |
May 27, 2023 |
Last update date |
May 29, 2023 |
Contact name |
Ximing Nian |
E-mail(s) |
nianximing@yeah.net
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Phone |
18759108482
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Organization name |
Shanghai Jiao Tong University
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Street address |
Chongqing Nanlu 227
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City |
shanghai |
State/province |
Shanghai |
ZIP/Postal code |
201600 |
Country |
China |
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Platform ID |
GPL24247 |
Series (1) |
GSE233613 |
Deletion of nucleoporin Seh1 impaired neurogenesis through transcriptional regulation (ChIP-Seq) |
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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 Selector |
Raw data are available in SRA |
Processed data provided as supplementary file |
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