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GSE280899

GSE GEO
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PUF60-Mediated Splicing Is a Key Driver of Triple Negative Breast Cancer

Organism: Homo sapiens
Platform: GPL24676
Samples: 112
Experiment Types:
Expression profiling by high throughput sequencing Other
Submitted: Nov 01 2024
Last Updated: Dec 15 2025
Status: Public on Dec 15 2025
Contact: Brian,,Yee (UCSD)

Relations

SuperSeries of: GSE280897 SuperSeries of: GSE280898 SuperSeries of: GSE313324 BioProject: https://www.ncbi.nlm.nih.gov/bioproject/PRJNA1181007

Summary

This SuperSeries is composed of the SubSeries listed below.

Overall Design

Refer to individual Series

Analysis (6 steps)

View Data Processing
Processing steps for GSE280899
  1. Reads were mapped using STAR 2.7.6a
  2. Read count extraction was performed using featureCounts from the Subread package.
  3. Results were sorted into counts matrices
  4. TPM was calculated manually from counts matrix
  5. Differential splicing analysis was performed on STAR-aligned reads using rMATS 4.0.2.
  6. For each condition, shRNA knockdown samples represent SAMPLE_1, while non-targeting controls (shNT1, shNT2, and shNT3) represent SAMPLE_2.
GEO Samples (112)
GSM8607229 GSM8607230 GSM8607231 GSM8607232 GSM8607233 GSM8607234 GSM8607235 GSM8607236 GSM8607237 GSM8607238 GSM8607239 GSM8607240 GSM8607241 GSM8607242 GSM8607243 GSM8607244 GSM8607245 GSM8607246 GSM8607247 GSM8607248 GSM8607249 GSM8607250 GSM8607251 GSM8607252 GSM8607253 GSM8607254 GSM8607255 GSM8607256 GSM8607257 GSM8607258 GSM8607259 GSM8607260 GSM8607261 GSM8607262 GSM8607263 GSM8607267 GSM8607268 GSM8607269 GSM8607270 GSM8607271 GSM8607272 GSM8607273 GSM8607274 GSM8607275 GSM8607276 GSM8607277 GSM8607278 GSM8607279 GSM8607280 GSM8607281 GSM8607282 GSM8607283 GSM8607284 GSM8607285 GSM8607286 GSM8607287 GSM8607288 GSM8607289 GSM8607290 GSM8607291 GSM8607292 GSM8617976 GSM8617977 GSM8617978 GSM8617979 GSM8617980 GSM9366194 GSM9366195 GSM9366196 GSM9366197 GSM9366198 GSM9366199 GSM9366200 GSM9366201 GSM9366202 GSM9366203 GSM9366204 GSM9366205 GSM9366206 GSM9366207 GSM9366208 GSM9366209 GSM9366210 GSM9366211 GSM9366212 GSM9366213 GSM9366214 GSM9366215 GSM9366216 GSM9366217 GSM9366218 GSM9366219 GSM9366220 GSM9366221 GSM9366222 GSM9366223 GSM9366224 GSM9366225 GSM9366226 GSM9366227 GSM9366228 GSM9366229 GSM9366230 GSM9366231 GSM9366232 GSM9366233 GSM9366234 GSM9366235 GSM9366236 GSM9366237 GSM9366238 GSM9366239

Linked Publications (3)

Integrative CRISPR Screening and RNA Analyses Discover an Essential Role for PUF60 Interactions with 3' Splice Sites in Cancer Progression.
Cancer research · 2025
Integrative CRISPR Screening and RNA Analyses Discover an Essential Role for PUF60 Interactions with 3' Splice Sites in Cancer Progression.
Cancer research · 2025
Flipper: An advanced framework for identifying differential RNA binding behavior with eCLIP data.
bioRxiv : the preprint server for biology · 2026