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Status |
Public on Apr 02, 2024 |
Title |
VSMC, miR-ctl, ChIP |
Sample type |
SRA |
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Source name |
vascular smooth muscle cell
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Organism |
Homo sapiens |
Characteristics |
cell type: vascular smooth muscle cell genotype: control antibody: anti-p53 antibody (Cat.ab1101, Lot.GR3436878-6, UK, Abcam)
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Extracted molecule |
genomic DNA |
Extraction protocol |
Cells were fixed with 1% fommaldehyde for 10 minutes. After guenching and cell lysis, Chromatin was sonicated using a Focused Ultrasonicator. ChlP-seg libraries were prepared using the KAPA Hyper Library Preparation Kit complemented with NEXTflex DNA Barcodes from Bio Scientific. 2-5 ng of DNA was used as starting material for input and ip samples. Libraries were amplified using 18 cycles on the themmocycler. Post amplification libraries were size selected at 200-500 bp in length using Agencout AMPure xP beads from Beckman couter. ibraries were valdalted using the kapa library quantification kit.
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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 |
Qualities off fastq files were inspected by fastqc (version 0.20.1). ChlP-seq reads were timmed from 3' end until the final base had a ouality score > 30. using trim_galore version 0.6.4_dev, discarding reads lelt with < 20 bp. The sequenced reads (FASTQ format) are mapped using tools such as Bowtie2 (Version 2.5.0). Bowtie2 can consider indels (insertions and deletions) by gapped alignments, which is appropriate for long and/or paired-end reads. After alignment, reads mapped to the same genomic positions are filtered as redundant reads, and the remaining nonredundant reads are used for analysis. The peak-calling step identifies significantly enriched loci (peaks) in the genome. All peak calling was performed with MACS2 (version 2.1.0) , While is the most commonly used peak-calling tool. Peak-calling results are generally returned in BED format. Assembly: hg38 Supplementary files format and content: bigwig,narrowpeak
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Submission date |
Feb 06, 2024 |
Last update date |
Apr 02, 2024 |
Contact name |
Jingsong Ou |
E-mail(s) |
oujs@mail.sysu.edu.cn
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Phone |
862087755766-8238
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Organization name |
The First Affiliated Hospital, Sun Yat-sen University
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Department |
Surgery/Cardiac Surgery
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Street address |
58 Zhong Shan Er Road
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City |
Guangzhou |
State/province |
Please Select |
ZIP/Postal code |
510080 |
Country |
China |
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Platform ID |
GPL24676 |
Series (1) |
GSE255157 |
Aging aggravates aortic aneurysm and dissection via miR-1204-MYLK signaling axis |
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Relations |
BioSample |
SAMN39842149 |
SRA |
SRX23548768 |
Supplementary file |
Size |
Download |
File type/resource |
GSM8064820_miR-ctl.bigwig |
93.4 Mb |
(ftp)(http) |
BIGWIG |
GSM8064820_miR-ctl.narrowPeak.gz |
1.5 Mb |
(ftp)(http) |
NARROWPEAK |
SRA Run Selector |
Raw data are available in SRA |
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