Bulk RNA‑seq of IMR90 fibroblasts in IR‑induced senescence with siRNA knockdowns of CCND1, CDK4, CDK6 and controls
RNA-seq (gene expression) · human · 21 samples
- What it is
- RNA-seq (gene expression)Gene activity measured by sequencing. The summary does not mention single-cell work, so this is most likely bulk: one average per sample, the usual starting point for comparing groups.
- Organism
- Homo sapiens (human)
- Samples
- 21 samples: 7 conditions, mostly in triplicateGroups are read from the sample names, not from the paper. Check the list below.
- Data you can get
- A processed table (series matrix) and supplementary files from NCBI; the raw sequencing reads from ENA. Which of these hold counts depends on the study, so check the file list.
- Paper
- Targeting CyclinD1-CDK6 to Mitigate Senescence-Driven Inflammation and Age-Associated Functional DeclinebioRxiv : the preprint server for biology · 2025
Direct links to NCBI and ENA, no account and no request form. Pick by what you want to do: take the small processed table to look, the supplementary files to re-analyse, or the original raw data to start over.
Processed table
The series matrix: one table of values per sample as the submitters processed it. The smallest download, and it opens in Excel or R. Start here to see what the data look like.
Supplementary files
The count tables and other files the authors uploaded. Take only the samples you need, or the whole study as GSE304266_RAW.tar (it can run to tens of gigabytes).
Raw sequencing reads
The original FASTQ files, straight from the sequencer, held at ENA. Large, and you align them yourself, so only choose this if you need to re-process the study from scratch.
What the files usually look like: For RNA-seq the counts are usually a table among the supplementary files (look for 'counts', 'expression', 'FPKM' or 'TPM' in the file name). The series matrix of a sequencing study is sometimes nearly empty.
Also filed as BioProject PRJNA1299856 and SRA study SRP605757. Searching any of these in the dataset finder brings you back here.
Supports a between-group comparison across 21 samples.
How we read this: 7 replicated groups read from 21 sample titles; they account for 21 of them. These groups are guessed from the sample names, not taken from the paper, so check them against the sample list below before relying on them.
- GSM9146428 Proliferating replicate1 Proliferating
- GSM9146429 Proliferating replicate2 Proliferating
- GSM9146430 Proliferating replicate3 Proliferating
- GSM9146431 Senescent Non targeting#3 knockdown, replicate1 Senescent Non targeting…
- GSM9146432 Senescent Non targeting#3 knockdown, replicate2 Senescent Non targeting…
- GSM9146433 Senescent Non targeting#3 knockdown, replicate3 Senescent Non targeting…
- GSM9146434 Senescent Non targeting#4 knockdown, replicate1 Senescent Non targeting…
- GSM9146435 Senescent Non targeting#4 knockdown, replicate2 Senescent Non targeting…
- GSM9146436 Senescent Non targeting#4 knockdown, replicate3 Senescent Non targeting…
- GSM9146437 Senescent CDK4 knockdown, replicate1 Senescent CDK4 knockdow…
- GSM9146438 Senescent CDK4 knockdown, replicate2 Senescent CDK4 knockdow…
- GSM9146439 Senescent CDK4 knockdown, replicate3 Senescent CDK4 knockdow…
- GSM9146440 Senescent CDK6 knockdown, replicate1 Senescent CDK6 knockdow…
- GSM9146441 Senescent CDK6 knockdown, replicate2 Senescent CDK6 knockdow…
- GSM9146442 Senescent CDK6 knockdown, replicate3 Senescent CDK6 knockdow…
- GSM9146443 Senescent CDK4, CDK6 dual knockdown, replicate1 Senescent CDK4, CDK6 du…
- GSM9146444 Senescent CDK4, CDK6 dual knockdown, replicate2 Senescent CDK4, CDK6 du…
- GSM9146445 Senescent CDK4, CDK6 dual knockdown, replicate3 Senescent CDK4, CDK6 du…
- GSM9146446 Senescent CCND1 knockdown, replicate1 Senescent CCND1 knockdo…
- GSM9146447 Senescent CCND1 knockdown, replicate2 Senescent CCND1 knockdo…
- GSM9146448 Senescent CCND1 knockdown, replicate3 Senescent CCND1 knockdo…
- GSE304272 Transcriptomic profiling of irradiated senescent IMR90 cells treated with CDK4/6 or JAK inhibitors 12 samples shares imr90, cdk4
- GSE295260 CDK4/6 inhibition induces a senescence-associated secretory phenotype via delayed NF-κB activation 40 samples shares cdk4, senescence
- GSE320212 Identifying Senescence and Immune Biomarkers Predictive of Benefit to Combined CDK4/6 and PD-1 Blockade in Dedifferentiated Liposarcoma: Single-Cell RNA-seq of Serial Tumor Biopsies 23 samples shares cdk4, senescence
- GSE233531 Dual inhibition of CDK4/6 and XPO1 induced senescence with acquired vulnerability to CRBN-based PROTAC drugs 10 samples shares cdk4, senescence
- GSE272306 RNA-seq of IMR90 senescence with CCF nuclear egress inhibition 9 samples shares imr90, senescence
- GSE295258 CDK4/6 inhibition induces a senescence-associated secretory phenotype via delayed NF-κB activation 54 samples shares cdk4, senescence
- GSE295261 CDK4/6 inhibition induces a senescence-associated secretory phenotype via delayed NF-κB activation [CUT&Tag] 24 samples shares cdk4, senescence
- GSE336040 CDK4/6 inhibition induces a senescence-associated secretory phenotype via delayed NF-κB activation [CUT&Run] 17 samples shares cdk4, senescence
Metadata from NCBI GEO, cached and refreshed periodically — the NCBI page above is authoritative. Downloads link straight to NCBI/ENA; nothing is proxied through BioTransfer.