| Experiment Id | GSE223049 | Name | Bulk RNA-seq in young (2 months) and aged (22-24 months) mice across 23 cell-types |
| Experiment Type | RNA-Seq | Study Type | Baseline |
| Source | GEO | Curation Date | 2025-01-03 |
| description | To understand how age rewires the chromatin accessibility landscape, we molecularly profiled 23 purified cell types from 11 tissues and organs by assessing the cumulative signature of 15-25 young and aged mice for robust difference detection. We performed RNA-seq for young (2 months) and aged (22-24 months) mice for FACS sorted cell-types. A 3-prime biased approach was used to generate sequencing libraries as described previously (Sun et al. Nat Comms 2021; https://doi.org/10.1038/s41467-021-22863-0). Barcoded 19bp R1 and 111bp R2 paired-end reads per sequencing lane were assigned to individual samples using the sabre software (version 80faf94) with options -u m 2 l 10" (https://github.com/najoshi/sabre) (Tsyganov et al. JOSS 2018; https://doi.org/10.21105/joss.00583). Here we present the single-end demultiplexed reads per sample which were mapped to the mouse GRCm38.p6/mm10 genome primary assembly using Spliced Transcripts Alignment to a Reference (STAR) software version 2.5.2b (Dobin et al. Bioinformatics 2013; https://doi.org/10.1093/bioinformatics/bts635). STAR was run with mode alignReads with parameters --outFileterMatchMinOverLred 0.3 --outFilerScoreMinOverLread 0.3 --twopassMode Basic sjdbGTFfile quanMode GeneCounts. Reads with duplicated UMIs were removed using the software Je version 2.0.RC option markdupes (Girardot et al. BMC Bioinformatics, 2016; https://doi.org/10.1186/s12859-016-1284-2). Transcript quantification was performed using featureCounts version 2.0.1 with parameters Q10 -M"" (exonic regions of GENCODEs vM24 annotation version) (Liao et al. NAR 2019; https://doi.org/10.1093/nar/gkz114). |
