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Sample GSM8064820 Query DataSets for GSM8064820
Status Public on Apr 02, 2024
Title VSMC, miR-ctl, ChIP
Sample type SRA
 
Source name vascular smooth muscle cell
Organism Homo sapiens
Characteristics cell type: vascular smooth muscle cell
genotype: control
antibody: anti-p53 antibody (Cat.ab1101, Lot.GR3436878-6, UK, Abcam)
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.
 
Library strategy ChIP-Seq
Library source genomic
Library selection ChIP
Instrument model Illumina NovaSeq 6000
 
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
 
Submission date Feb 06, 2024
Last update date Apr 02, 2024
Contact name Jingsong Ou
E-mail(s) oujs@mail.sysu.edu.cn
Phone 862087755766-8238
Organization name The First Affiliated Hospital, Sun Yat-sen University
Department Surgery/Cardiac Surgery
Street address 58 Zhong Shan Er Road
City Guangzhou
State/province Please Select
ZIP/Postal code 510080
Country China
 
Platform ID GPL24676
Series (1)
GSE255157 Aging aggravates aortic aneurysm and dissection via miR-1204-MYLK signaling axis
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 SelectorHelp
Raw data are available in SRA

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