Comment[GEAAccession]	E-GEAD-391
MAGE-TAB Version	1.1
Investigation Title	Pericentromeric noncoding RNA drives the 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 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 and chromosomal alteration in SVts8 cells, a conditionally immortalized human fibroblast cell line.
Experimental Design	genetic modification 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	2024-08-28
Protocol Name	P-GEAD-616	P-GEAD-617	P-GEAD-618	P-GEAD-619	P-GEAD-620
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 or TIG3 cells were cultured in DME medium (Nacalai tesque) supplemented with 10% FBS and penicillin/streptomycin (Sigma-Aldrich) at 5% CO2 condition.	Cells at 70-80% confluency were trypsinized, then 50,000 viable cells were suspended in ATAC-Resuspension Buffer as described previously (Corces et al., Nature Methods, 2017).	Suspended cells were resuspended in transposition mixture and incubated at 37 degree for 30 min, then the transposed fragments were cleaned using DNA Clean & Concentrator-5 Kit and amplified using NEBNext High-Fidelity 2X PCR Master Mix with indicated primers as described previously (Corces et al., Nature Methods, 2017).	The amplicon libraries for sequencing were quantified using a LabChip GX Touch (PerkinElmer), KAPA Library Quantification Kit (KAPA Biosystems, #KK4824), and sequenced using 2 x 75-bp MiSeq Reagent kits v3 (illumina) on an Illumina MiSeq.	resulting Fastq reads underwent quality control with FastQC (version 0.11.8) and were trimmed with Trimglore (version 0.6.4). The trimmed sequences were mapped against H. sapiens UCSC hg19 using the Bowtie 2 (version 2.3.5) alignment software. Uniquely mapped reads were used for peak calling using MACS (version 2.1.4) with the command $ macs2 callpeak --nomodel --nolambda --keep-dup all --call-summits -f BAMPE -g hs, and peaks were filtered by enrichment score (q < 0.01)
SDRF File	E-GEAD-391.sdrf.txt
Comment[AEExperimentType]	ATAC-seq
Comment[BioProject]	PRJDB10513
Comment[Last Update Date]	2024-08-28