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Sample GSM8227104 Query DataSets for GSM8227104
Status Public on Sep 13, 2024
Title HDF-siControl-replicate_IP
Sample type SRA
 
Source name primary human dermal fibroblasts
Organism Homo sapiens
Characteristics cell line: primary human dermal fibroblasts
cell type: fibroblasts
genotype: siControl
merip antibody: m6A
Treatment protocol Transfection of scramble siRNA or ALKBH5 knockdown siRNA
Extracted molecule total RNA
Extraction protocol Total RNA was extracted using TRIzol reagent (Solarbio, USA).
further transcriptome-wide interrogation was pursued by deep sequencing using SMARTer Stranded Total RNA-Seq Kit version 2 (Pico Input Mammalian; 634413; Takara/Clontech, Japan) according to the manufacturer's protocol.
 
Library strategy OTHER
Library source transcriptomic
Library selection other
Instrument model Illumina NovaSeq 6000
 
Description For Merip-Seq
SiNC_2-IP
Data processing library strategy: meRIP-seq
Raw reads in fastq format were processed to remove contaminating adapter sequences using Trimmomatics
Quality distribution plot and base content distribution were generated by FASTQC
MeRIPseq reads were aligned to the hg38 genome using STAR.
m6A Peaks were called uing MetPeak with the significance cut-off p-value <=0.05
Assembly: hg38
Supplementary files format and content: BED (except for Input sample)
 
Submission date Apr 24, 2024
Last update date Sep 13, 2024
Contact name Ruoqing Xu
E-mail(s) annahsu996@gmail.com, ruoqing_xu@sjtu.edu.cn, annahsu@163.com
Phone +8615927673283
Organization name Shanghai Ninth People's Hospital, Shanghai Jiao Tong University School of Medicine.
Department Department of Plastic and Reconstructive Surgery
Street address Department of Plastic and Reconstructive Surgery, Shanghai Ninth People’s Hospital, Shanghai Jiao Tong University School of Medicine, 639 Zhizaoju Road, Shanghai, P.R. China
City Shanghai, China
ZIP/Postal code 200011
Country China
 
Platform ID GPL24676
Series (1)
GSE264743 ALKBH5-mediated m6A demethylation ameliorates extracellular matrix deposition in cutaneous pathological fibrosis [meRIP-seq]
Relations
BioSample SAMN41069210
SRA SRX24353746

Supplementary file Size Download File type/resource
GSM8227104_SiNC_2-IPVSSiNC_2-input.final.bed.gz 221.3 Kb (ftp)(http) BED
SRA Run SelectorHelp
Raw data are available in SRA

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