|
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 |