biostudies-arrayexpressSivarajan KarunanithiHomo sapienshttps://www.ebi.ac.uk/biostudies/studies/E-MTAB-15914The accumulation of senescent cells constitutes a pivotal hallmark of tissue ageing, contributing to disruption of tissue homeostasis and thus, to the development of several aging-related diseases. We employ transcriptomics (alongside proteomics) to determine changes at the mRNA and protein levels, during replicative senescence in human IMR90 fibroblasts.biostudies-arrayexpressLibrary Construction - NGS libraries were prepared using Illumina's Stranded mRNA Prep Ligation Kit following Stranded mRNA Prep Ligation Reference Guide (April 2021) (Document 1000000124518 v02). Libraries were prepared with a starting amount of 500ng and amplified in 10 PCR cycles. Two post PCR purification steps were performed to exclude residual primer and adapter dimers. Libraries were profiled with a DNA 1000 chip on a 2100 Bioanalyzer (Agilent technologies) and quantified using the Qubit 1x dsDNA HS Assay Kit, in a Qubit 4.0 Fluorometer (Invitrogen by Thermo Fisher Scientific, USA).Sequencing - All 12 samples were pooled in equimolar ratio and sequenced on 1 NextSeq2000 P2 (100cycles) FC, SR for 1x 116 cycles plus 2x 10 cycles for the dual index read and 1 dark cycle upfront R1.Growth Protocol - Human embryonic lung fibroblasts (IMR90 cells) were obtained from the Coriell institute for medical research (Camden, NJ, USA), and maintained in Dulbecco’s modified Eagle’s medium (Invitrogen) supplemented with 10% fetal bovine serum (v/v), 1 mM sodium pyruvate (GibcoTM, 11360-070, Thermo Fisher Scientific, USA) , 1x MEM non-essential amino acids (GibcoTM, 1140-035, Thermo Fisher Scientific, USA) and 1x antibiotic-antimycotic mixture (GibcoTM, 1760-250106, Thermo Fisher Scientific, USA). Cells were maintained at 37◦C in a humidified atmosphere in 5% CO2 and sub-cultured at a confluency of 80%. Cell numbers were assessed by manual counting using a Neubauer Chamber, at least in triplicates. Population doubling was tracked according to the following formula: log2(collected)Sample Collection - Human embryonic lung fibroblasts (IMR90 cells) were obtained from the Coriell institute for medical research (Camden, NJ, USA), and maintained in Dulbecco’s modified Eagle’s medium (Invitrogen) supplemented with 10% fetal bovine serum (v/v), 1 mM sodium pyruvate (GibcoTM, 11360-070, Thermo Fisher Scientific, USA) , 1x MEM non-essential amino acids (GibcoTM, 1140-035, Thermo Fisher Scientific, USA) and 1x antibiotic-antimycotic mixture (GibcoTM, 1760-250106, Thermo Fisher Scientific, USA). Cells were maintained at 37◦C in a humidified atmosphere in 5% CO2 and sub-cultured at a confluency of 80%. Cell numbers were assessed by manual counting using a Neubauer Chamber, at least in triplicates. Population doubling was tracked according to the following formula: log2(collecteSample Treatment - Cells were passaged at 80% confluency and harvested at the indicated population doublings.Nucleic Acid Extraction - RNA was extracted using the Qiagen RNeasy Plus Mini Kit (QIAGEN, Netherlands), following the manufacturer’s instructions. Residual DNA was removed using the gDNA eliminator columns from the kit. RNA concentration and quality was further evaluated using A280/260 absorbance (Nanodrop) and the Agilent RNA 6000 Nano Kit (using manufacturer’s instructions, using the Bioanalyser).OrganizationMINSEQE ScoreAssays and DataProcessed DataMAGE-TAB FilesData Transformation - The pairwise differential expression analysis of the age groups was performed in R (v4.1.1) with the DESeq2 (v.1.33.5) R package. The genes were subjected to pairwise differential expression analysis, comparing consecutive and extreme timepoints of the growth curve, and a fold change ±1.1 and an FDR<0.01 was established as a cut-off for significant regulation. Additionally, a likelihood ratio test was performed using the DESeq2 (v1.44.0) package to identify genes that are differentially expressed across all age groups, using and adjusted p-value of 0.01 as a cut-off for statistical significance.Sequence Alignment - Reads were quality controlled using FastQC (v0.11.9), (https://www.bioinformatics.babraham.ac.uk/projects/fastqc/). Reads were mapped to the reference genome (GRCh38; release 84) using STAR (v2.7.3a) with default parameters (except --outFilterMismatchNoverLmax 0.04 and --outFilterMismatchNmax 999). Using only the uniquely mapped reads, gene level read summarization was performed using subread featureCounts (v.2.0.0) with the canonical annotation (GRCh38; v98).MetabolomicsUnknownTranscriptomicsGenomicsProteomicsNextSeq 2000RNA-seq of coding RNAHomo sapiensQuantitative proteomics reveals coordinated changes in the proteome during replicative senescenceNádia Da Silva FernandesChristian BehlSivarajan KarunanithiAmitkumar FulzeleNádia Da Silva Fernandes, Fridolin Kielisch, Amitkumar Fulzele, Sivarajan Karunanithi, Justus F. Gräf, Jia-Xuan Chen, Christian Behl, Helle D. Ulrich, Petra BeliHelle UlrichPetra BeliJia-Xuan ChenJustus GrafFridolin KielischfalseTranscriptomics of human IMR90 model of replicative senescenceThe accumulation of senescent cells constitutes a pivotal hallmark of tissue ageing, contributing to disruption of tissue homeostasis and thus, to the development of several aging-related diseases. We employ transcriptomics (alongside proteomics) to determine changes at the mRNA and protein levels, during replicative senescence in human IMR90 fibroblasts.2026-07-16T00:00:00Z2026-07-16T13:34:52.259Z2025-10-29T13:02:20.124ZE-MTAB-15914ERP183289EFO_0002944EFO_0004170EFO_0003789EFO_0004917EFO_0005518EFO_0003816EFO_0003738EFO_0004184EFO_0003969