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| Status |
Public on Apr 14, 2024 |
| Title |
hinput |
| Sample type |
SRA |
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| Source name |
Ovary
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| Organism |
Homo sapiens |
| Characteristics |
tissue: Ovary
cell line: KGN cell
cell type: human granulosa cells
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| Growth protocol |
DMEM/F12, 10% fetal bovine serum, 1x penicillin/streptomycin. Cells were cultured at 37℃ at 5% CO2.
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| 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.
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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 |
Raw data (raw reads) of fastq format were firstly processed using fastp (version 0.19.11) 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. Index of the reference genome was built using BWA (v 0.7.12) and clean reads were aligned to the reference genome using BWA mem (v 0.7.12).
For a specific ChIP-seq binding site, individual reads mapping to the plus or minus strand and present significant enrich. For single-end sequencing, the fragment size was estimated with MACS2 predicted method with default parameters. MACS2 scan all the genome with a specific window size and calculate the reads enrichment level. A particular number of windows were used as samples to build enrichment model and to predict fragment size. The following peak calling analysis was based on this predicted fragment size.
After mapping reads to the reference genome, we used the MACS2 (version 2.1.0) peak calling software to identify regions of IP enrichment over background. A q-value threshold of 0.05 was used for all data sets. After peak calling, the distribution of chromosome distribution, peak width, fold enrichment, significant level and peak summit number per peak were all displayed.
The interaction between transcript factor or chromatin histone modification and DNA were not random, while they show some specific sequence preference. Homer was used to detect the denovo sequence motif and the matched known motifs.
Assembly: hg38
Supplementary files format and content: bigWig, narrowPeak
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| Submission date |
Apr 09, 2024 |
| Last update date |
Apr 14, 2024 |
| Contact name |
Nianyu Li |
| E-mail(s) |
201915231@mail.sdu.edu.cn
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| Phone |
17854225129
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| Organization name |
Shandong University
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| Street address |
44 wenhua xi road
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| City |
Jinan |
| State/province |
ShanDong |
| ZIP/Postal code |
250012 |
| Country |
China |
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| Platform ID |
GPL24676 |
| Series (1) |
| GSE263539 |
ChIP-seq analysis of G3BP1 in KGN cells |
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| Relations |
| BioSample |
SAMN40894094 |
| SRA |
SRX24196610 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSM8194153_hinput.bw |
101.9 Mb |
(ftp)(http) |
BW |
SRA Run Selector |
| Raw data are available in SRA |
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