Comment[GEAAccession]	E-GEAD-345
MAGE-TAB Version	1.1
Investigation Title	Pericentromeric noncoding RNA drives the expression of senescence-associated secretory phenotype
Experiment Description	Aging is one of the risk factors for cancer development because the accumulation of senescent cells during the aging process contributes to a various age-related pathologies through senescence-associated secretory phenotype (SASP). Therefore, an understanding of the molecular mechanism involved in SASP regulation could have a tremendous impact on our health. Here, we discovered that noncoding RNA derived from normally silenced pericentromeric repetitive sequences during cellular senescence, and analyzed the effect of the RNA on gene expression in SVts8 cells, a conditionally immortalized human fibroblast cell line.
Experimental Design	strain or line design
Experimental Factor Name	overexpression
Experimental Factor Type	overexpression
Person Last Name	Miyata	Takahashi
Person First Name	Kenichi	Akiko
Person Affiliation	Project for Cellular Senescence, Cancer Institute, Japanese Foundation for Cancer Research	
Person Roles	submitter	submitter
Public Release Date	2024-03-09
Protocol Name	P-GEAD-375	P-GEAD-376	P-GEAD-377	P-GEAD-378	P-GEAD-379
Protocol Type	sample collection protocol	nucleic acid extraction protocol	nucleic acid library construction protocol	nucleic acid sequencing protocol	normalization data transformation protocol
Protocol Description	SVts8 cells were cultured in DME medium (Nacalai tesque) supplemented with 10% FBS and penicillin/streptomycin (Sigma-Aldrich) at 5% CO2 condition.	Total RNA was extracted from SVts8 cells using TRIzol Reagent (Invitrogen), then removed the genomic DNA by TURBO DNA-free Kit (Applied Biosystems).	Libraries from DNased RNA for next generation sequence were prepared using NEBNext Ultra RNA Library Prep Kit for llumina (NEB).	Prepared and quantified libraries were sequenced by 150 bp paired-end on a HiSeq X instruments at AnnoRoad Corporation.	Resulting Fastq reads underwent quality control with FastQC (version 0.11.8), then some reads containing more than 50% of below Q20 and more than 5% of N were removed. The trimmed reads were aligned to H. sapiens UCSC hg19 using HISAT2 (version 2.1.0) in a default setting, then FPKM (fragments per kilobase of exon per million reads mapped) were estimated by StringTie (version 2.0).
SDRF File	E-GEAD-345.sdrf.txt
Comment[AEExperimentType]	RNA-seq of coding RNA
Comment[BioProject]	PRJDB9443
Comment[Last Update Date]	2024-03-09