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GSE222217

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Remodeling oncogenic transcriptomes by small molecules targeting NONO

Organism: Homo sapiens
Platform: GPL20301
Samples: 81
Experiment Types:
Expression profiling by high throughput sequencing
Submitted: Jan 05 2023
Last Updated: Jun 20 2023
Status: Public on Mar 21 2023
Contact: Garrett,Lee,Lindsey (Scripps Research)

Relations

SuperSeries of: GSE198419 SuperSeries of: GSE222216 BioProject: https://www.ncbi.nlm.nih.gov/bioproject/PRJNA918613

Summary

This SuperSeries is composed of the SubSeries listed below.

Overall Design

Refer to individual Series

Analysis (7 steps)

View Data Processing
Processing steps for GSE222217
  1. For differential expression:
  2. Transcript abundance was quantified using Salmon [v1.3.0] with GENCODE v37 annotation.
  3. Gene level quantification was performed using tximeta [v1.8.4].
  4. Differential gene expression was analyzed by DESeq2 [v1.30.1].
  5. For splicing analysis, 22Rv1 data only:
  6. RNA-seq reads were mapped to hg38 using STAR Aligner.
  7. Alternative splicing (AS) analysis was completed using rMATs (v3.2.5).
GEO Samples (81)
GSM5946440 GSM5946441 GSM5946442 GSM5946443 GSM5946444 GSM5946445 GSM5946446 GSM5946447 GSM5946448 GSM5946449 GSM5946450 GSM5946451 GSM5946452 GSM5946453 GSM5946454 GSM5946455 GSM5946456 GSM5946457 GSM5946458 GSM5946459 GSM5946460 GSM5946461 GSM5946462 GSM5946463 GSM5946464 GSM5946465 GSM5946466 GSM5946467 GSM5946468 GSM5946469 GSM5946470 GSM5946471 GSM5946472 GSM5946473 GSM5946474 GSM5946475 GSM6918081 GSM6918082 GSM6918083 GSM6918084 GSM6918085 GSM6918086 GSM6918087 GSM6918088 GSM6918089 GSM6918090 GSM6918091 GSM6918092 GSM6918093 GSM6918094 GSM6918095 GSM6918096 GSM6918097 GSM6918098 GSM6918099 GSM6918100 GSM6918101 GSM6918102 GSM6918103 GSM6918104 GSM6918105 GSM6918106 GSM6918107 GSM6918108 GSM6918109 GSM6918110 GSM6918111 GSM6918112 GSM6918113 GSM6918114 GSM6918115 GSM6918116 GSM6918117 GSM6918118 GSM6918119 GSM6918120 GSM6918121 GSM6918122 GSM6918123 GSM6918124 GSM6918125

Dataset Citations (1)

Remodeling oncogenic transcriptomes by small molecules targeting NONO.
PMID 36864190 · 2023 · Nature chemical biology
Stefan G Kathman, Seong Joo Koo, Garrett L Lindsey, Hsuan-Lin Her, Steven M Blue, Haoxin Li, Steffen Jaensch, Jarrett R Remsberg, Kay Ahn, Gene W Yeo, Brahma Ghosh, Benjamin F Cravatt

Linked Publications (2)

Remodeling oncogenic transcriptomes by small molecules targeting NONO.
Nature chemical biology · 2023
Remodeling oncogenic transcriptomes by small molecules targeting NONO.
Nature chemical biology · 2023