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| Status |
Public on Sep 18, 2023 |
| Title |
2-2-ip |
| Sample type |
SRA |
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| Source name |
Brain
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| Organism |
Mus musculus |
| Characteristics |
tissue: Brain
cell line: Neuro-2a
cell type: mouse neuroblastoma N2a cells
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| Treatment protocol |
For infection, cells were infected with ICP0-null HSV-1 (7134) for 5hpi (MOI = 3) before ChIP-seq
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| Extracted molecule |
genomic DNA |
| Extraction protocol |
Cell monolayers in 100-mm plates were crosslinked in 1% formaldehyde for 10 min at room temperature, quenched with 0.125 M of glycine for 5 min, washed twice with 5 ml of cold PBS. The cells were then scraped into 15 ml tubes with 8 ml of cold PBS and spinned at 2000 rpm for 5 min at 4°C. The supernatant was discarded and the cell pellet was store at -80C. On the day of sonication, the cells were lysed for 30 min on ice in 300 ul of 0.4% SDS lysis buffer (1% SDS, 10 mM of EDTA, 50 mM of Tris, pH 8.0) and transferred into 1.5 ml Eppendorf tubes. The cell lysate was sonicated on ice using a Ultrasonic Homogenizer SCIENTZ-IID for 10 cycles of 1 min each on the setting of 30 s ON, 30 s OFF and 80 watts.
the purified DNA was used NEBNext® Ultra™ II DNA Library Prep Kit (catalogue no. E7645L; NEB) for ChIP-seq library preparation.
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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 |
Real-Time Analysis(v3.4.4) and bcl2fastq(v2.19) softwares used for basecalling.
Reads containing adapter contamination, low-quality nucleotides and unrecognizable nucleotide were discarded to obtain clean reads using fastp (version 0.23.1).
The clean reads were aligned to the reference genome using alignment algorithms Bowtie2 (version 2.3.4.3) with default parametres.
The virus and mouse reads were splited. DeepTools (verison 3.5.1) bamCoverage was used to calculated the read coverage, plotProfiles and computeMatrix were utilized to plot signals around the reference-point of TSS. Peak calling algorithms, MACS2 (version 2.2.7.1), were used to identify significant peaks representing protein-DNA binding sites for mouse and virus seperately.
The peaks were annotated to known genomic features using ChIPseeker (version 1.32.1). Homer2 (version 4.11.1) findMotifsGenome.pl was the used to enrich the known and de novo motifs. Integrative Genomics Viewer (IGV) was used to visualize the read coverage and the identified peaks.
Assembly: mm10
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| Submission date |
Aug 29, 2023 |
| Last update date |
Sep 18, 2023 |
| Contact name |
Xiang Yuhang |
| E-mail(s) |
[email protected]
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| Phone |
13260557905
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| Organization name |
none
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| Street address |
Yuhang Tang street
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| City |
Hangzhou |
| ZIP/Postal code |
310000 |
| Country |
China |
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| Platform ID |
GPL24247 |
| Series (1) |
| GSE241863 |
Identification of the binding DNA of ONECUT2 by ChIP in Neuro-2a cells |
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| Relations |
| BioSample |
SAMN37186787 |
| SRA |
SRX21504341 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSM7744659_2-2-IP.sorted.bw |
130.2 Mb |
(ftp)(http) |
BW |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data provided as supplementary file |
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