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| Status |
Public on Jun 01, 2024 |
| Title |
IgG_2 |
| Sample type |
SRA |
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| Source name |
Immortalized dendritic cells
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| Organism |
Mus musculus |
| Characteristics |
strain: C57BL/6
treatment: untreated
chip antibody: Normal Rabbit IgG (#2729, CST)
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| Growth protocol |
Mutu DC1940 cells were cultured in IMDM Modified (Hyclone, with HEPES) media supplemented with 10% FBS, 100 U/mL penicillin (Gibco), 100 U/mL streptomycin (Gibco) and 50 µM β-Mercaptoethanol.
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| Extracted molecule |
genomic DNA |
| Extraction protocol |
For each biological repeat, 2×10^7 cells were cross-linked with 1 % formaldehyde at room temperature for 10 min and quenched with 0.125 M glycine. Samples were further sonicated and enzyme-sheared with the ChIP-IT® Express Enzymatic Shearing Kit (#53035, Active Motif). Chromatin from 5×10^6 cells were incubated with 5µg antibody or IgG at 4 ℃ overnight, followed by purification of IP product with the Magna ChIP™ Protein A+G magnetic beads (#16-663, Millipore) , de-crosslinking, and extraction with the MinElute PCR purification kit (#28004, Qiagen).
The libraries were constructed by Novogene Corporation (Beijing, China) using standard Illumina 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 |
Raw reads in FASTQ format were processed through fastp (v0.19.11) to remove adapter-containing, poly-N containing, or low-quality reads in order to generate clean data.
Index of the reference genome (mm10) was built using BWA (v 0.7.12), and clean reads were aligned to the reference genome using BWA-MEM(v 0.7.12).
The bamCoverage tool (v2.2) of Deeptools was used to generate bigWig files.
Genome_build: mm10
Supplementary_files_format_and_content: Processed data are in bigWig format for graphic display of genomic binding sites.
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| Submission date |
Jan 18, 2022 |
| Last update date |
Jun 01, 2024 |
| Contact name |
Xiangyi Shen |
| E-mail(s) |
[email protected]
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| Organization name |
Tsinghua University
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| Department |
The Institute for Immunology, School of Medicine
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| Street address |
D303 Zhengyutong Medical Building, Tsinghua University
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| City |
Beijing |
| ZIP/Postal code |
100084 |
| Country |
China |
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| Platform ID |
GPL24247 |
| Series (1) |
| GSE193918 |
Genome-wide map of TRIM33 binding sites in the dendritic cell line Mutu DC1940 |
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| Relations |
| BioSample |
SAMN25068095 |
| SRA |
SRX13823001 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSM5823637_IgG_2.bw |
146.2 Mb |
(ftp)(http) |
BW |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data provided as supplementary file |
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