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| Status |
Public on Dec 31, 2023 |
| Title |
ChIP-IgG-LPS-plus-OTX015 |
| Sample type |
SRA |
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| Source name |
THP1
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| Organism |
Homo sapiens |
| Characteristics |
antibody: BRD3
cell line: THP1
cell type: Human monocytes
genotype: WT
treatment: lipopolysaccharide+OTX015
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| Treatment protocol |
lipopolysaccharide (100ng/ml) for 1h
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| Growth protocol |
THP1 monocytes were maintained in RPMI 1640 supplemented with 10% fetal bovine serum (FBS) and antibiotics in humidified atmosphere with 5% CO2 at 37C
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| Extracted molecule |
genomic DNA |
| Extraction protocol |
Cells were fixed with 1% formaldehyde for 10 minutes, After quenching the cell lysis, chromatin was sonicated using E220 focused-ultrasonicator.
ChIP-seq libraries were prepared using the KAPA HTP library,preparation kit complemented with NEXTflex DNA Barcodes from Bioo Scientific. 10 ng of DNA was used as starting material for input and IP samples. Libraries was amplified using 13 cycles on the thermocycler. Post amplification libraries were size selected at 250-450 bp in length using Agencourt AMPure XP beads from Beckman Coulter. Libraries were validated using the Agilent High Sensitivity DNA kit.
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| Library strategy |
ChIP-Seq |
| Library source |
genomic |
| Library selection |
ChIP |
| Instrument model |
Illumina NextSeq 500 |
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| Data processing |
Basecalls were performed using bcl2fastq v2.17 for Novaseq output.
ChIP-seq reads were trimmed from 3' end until the final base has a quality score>30, using Trimmomatic v0.33, discarding reads left with <20 bp
ChIP-seq reads were aligned to the UCSC hg38 genome using Bowtie version 1.1.2. Only uniquely mapping reads with at most two mismatches were retained.
To creat ChIP-seq coverage plots, the locations of the mapped ChIP-seq reads were extended to 150 bp to represent sequenced fragments, renormalized (to reads per million, rpm) and reformation in the bigwig file format.
bigWig files were generated using the genomicRanges R package. Score represents the normalized coverage of DNA fragments at a given genomic coordinate. gappedPeak files were generated using MACS v2 with default settings.
Assembly: hg38
Supplementary files format and content: bigWig, gappedpeak
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| Submission date |
Jun 05, 2023 |
| Last update date |
Dec 31, 2023 |
| Contact name |
Nian Wang |
| E-mail(s) |
nianwang222@gmail.com
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| Organization name |
Central south university
|
| Street address |
No.110 Xiangya Road
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| City |
Changsha |
| State/province |
Hunan |
| ZIP/Postal code |
410078 |
| Country |
China |
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| Platform ID |
GPL18573 |
| Series (1) |
| GSE234162 |
Decoding the gene promoters binding with BRD3 in LPS-primed THP1 monocytes |
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| Relations |
| BioSample |
SAMN35626132 |
| SRA |
SRX20595944 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSM7450012_ChIP-IgG-LPS-plus-OTX015_R1.bigWig |
356.0 Mb |
(ftp)(http) |
BIGWIG |
| GSM7450012_ChIP-IgG-LPS-plus-OTX015_R1_peaks.gappedPeak.gz |
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(ftp)(http) |
GAPPEDPEAK |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data provided as supplementary file |
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