About our database

This database is comprised of senescent human fibroblast transcriptome data across all experimentally explored timepoints.

 

To be included in the database, studies had to be unbiased transcriptomic studies in senescent human fibroblasts; data had to be RNAseq or microarray data stored in GEO or Array Express; each condition in a dataset needed at least 2 repeats. Studies which met the above criteria were further filtered and any which met specific exclusion criteria were excluded.

Exclusion criteria included experiments been performed at the single cell level, two-colour or custom microarrays used in microarray studies, or data could not be downloaded from GEO or Array Express and the authors were unable to supply the data prior to our deadline date.

For further details on the systematic review and the inclusion/exclusion criteria, please consult the publication associated with the database creation listed below.

 

The database contains (last updated 05-Oct-2023):

  • 119 studies
    • There are a total of 1069 sample comparisons from these 119 studies
    • Comparisons means, for example, a cell which has been induced to enter senescence via DNA damage at day 6 post-senescence induction versus a proliferating control cell, or a DDIS cell which has siRNA treatment versus a DDIS cell without siRNA treatment
  • 14 types of senescence
  • 4 non-senescent control conditions
  • 17 fibroblast cell lines
    • With tissue origin as either the skin or lungs
  • The timeframe post-senescence induction spans from day 0 to day 112
    • Most samples are analysed between days 0 and 11 post-senescence induction
    • All samples analysed after day 28 are only in REP

 

To keep the database up to date, GEO and Array Express will be regularly searched against our specified criteria for new publications which can be uploaded to the website.

 

Publication associated with the creation of this database:

Scanlan et al, 2022. doi: https://doi.org/10.1101/2022.08.16.504144

 

Database created and maintained by the Shanley lab group at Newcastle University.