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GSE220185

GSE GEO
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Proteomic discovery of chemical probes that perturb protein complexes in human cells

Organism: Homo sapiens
Platform: GPL24676
Samples: 16
Experiment Types:
Other
Submitted: Dec 06 2022
Last Updated: Apr 15 2023
Status: Public on Apr 13 2023
Contact: Hsuan-Lin,,Her (UCSD)

Relations

BioProject: https://www.ncbi.nlm.nih.gov/bioproject/PRJNA909188

Summary

Most proteins in the human proteome lack chemical probes, and several large-scale and generalizable small-molecule binding assays have been introduced to address this problem. How compounds discovered in such “binding-first” assays affect protein function, nonetheless, often remains unclear. Here, we describe a “function first” proteomic strategy that uses size exclusion chromatography (SEC) to assess the global impact of electrophilic compounds on protein complexes in human cells. Integrating the SEC data with cysteine-directed activity-based profiling identifies changes in protein-protein interactions that are caused by site-specific liganding events, including the stereoselective engagement of cysteines in PSME1 and SF3B1 that disassemble the PA28 proteasome regulatory complex and remodel the spliceosome, respectively. Our findings thus show how multidimensional proteomic analysis of focused libraries of electrophilic compounds can expedite the discovery of chemical probes with site-specific functional effects on protein complexes in human cells. In this experiment, we probed the RNA-binding profile of DDX42 by eCLIP via an endogenously introduced HA-tag in the context of various SF3B1 ligands.

Overall Design

Two independent treatments were performed for each of 4 treatment groups (3h DMSO, 5uM WX-02-23, 5uM WX-02-43, 100nM PladB). An input and an eCLIP fraction were sequenced for each individual replicate, yielding a total of 16 samples.

Analysis (4 steps)

View Data Processing
Processing steps for GSE220185
  1. Processed using Skipper https://github.com/YeoLab/skipper
  2. Skipper trims the read, extract UMI, align to the genome and deduplicate
  3. To find enriched windows, it models the CLIP libraries crosslinking-induced truncation(CITs) with beta-binomial model with GC-bias of each window as a varaible
  4. overdispersion parameters are estimated from two input replicates

Supplementary Files (5)

GSE220185_DDX42_DMSO.reproducible_enriched_windows.tsv.gz Download
GSE220185_DDX42_PladB.reproducible_enriched_windows.tsv.gz Download
GSE220185_DDX42_WX-2-23.reproducible_enriched_windows.tsv.gz Download
GSE220185_DDX42_WX-2-43.reproducible_enriched_windows.tsv.gz Download
GSE220185_RAW.tar Download
GEO Samples (16)
GSM6793353 GSM6793354 GSM6793355 GSM6793356 GSM6793357 GSM6793358 GSM6793359 GSM6793360 GSM6793361 GSM6793362 GSM6793363 GSM6793364 GSM6793365 GSM6793366 GSM6793367 GSM6793368

SRA Experiments (16) and Runs (16)

Total: 13719 MB
SRX18508199 SRP411598 RIP-Seq SINGLE
GSM6793353: DDX42 SMInput treated with DMSO (rep1); Homo sapiens; RIP-Seq
Sample: SRS15977286
BioProject: PRJNA909188
BioSample: SAMN32069685
Platform: ILLUMINA
Instrument: Illumina NovaSeq 6000
Organism: Homo sapiens
Sample attributes
source_name: HCT116 colon cancer cell line
cell type: HCT116, DDX42 HA-tagged
treatment: DMSO
clip antibody: none (input)
Original files (1)
HCT116 colon cancer cell line
Runs (1)
Run Spots Bases Size (MB) Files Link
SRR22544231 33208148 3320814800 1056.61 DDX42_DMSO.Input1.fastq.gz, SRR22544231, SRR22544231.lite SRA
SRX18508200 SRP411598 RIP-Seq SINGLE
GSM6793354: DDX42 CLIP treated with DMSO (rep1); Homo sapiens; RIP-Seq
Sample: SRS15977287
BioProject: PRJNA909188
BioSample: SAMN32069684
Platform: ILLUMINA
Instrument: Illumina NovaSeq 6000
Organism: Homo sapiens
Sample attributes
source_name: HCT116 colon cancer cell line
cell type: HCT116, DDX42 HA-tagged
treatment: DMSO
clip antibody: CST #3724S
Original files (1)
HCT116 colon cancer cell line
Runs (1)
Run Spots Bases Size (MB) Files Link
SRR22544230 50851230 5085123000 1625.03 DDX42_DMSO.CLIP1.fastq.gz, SRR22544230, SRR22544230.lite SRA
SRX18508201 SRP411598 RIP-Seq SINGLE
GSM6793355: DDX42 SMInput treated with DMSO (rep2); Homo sapiens; RIP-Seq
Sample: SRS15977288
BioProject: PRJNA909188
BioSample: SAMN32069683
Platform: ILLUMINA
Instrument: Illumina NovaSeq 6000
Organism: Homo sapiens
Sample attributes
source_name: HCT116 colon cancer cell line
cell type: HCT116, DDX42 HA-tagged
treatment: DMSO
clip antibody: none (input)
Original files (1)
HCT116 colon cancer cell line
Runs (1)
Run Spots Bases Size (MB) Files Link
SRR22544229 24047937 2404793700 770.27 DDX42_DMSO.Input2.fastq.gz, SRR22544229, SRR22544229.lite SRA
SRX18508202 SRP411598 RIP-Seq SINGLE
GSM6793356: DDX42 CLIP treated with DMSO (rep2); Homo sapiens; RIP-Seq
Sample: SRS15977289
BioProject: PRJNA909188
BioSample: SAMN32069682
Platform: ILLUMINA
Instrument: Illumina NovaSeq 6000
Organism: Homo sapiens
Sample attributes
source_name: HCT116 colon cancer cell line
cell type: HCT116, DDX42 HA-tagged
treatment: DMSO
clip antibody: CST #3724S
Original files (1)
HCT116 colon cancer cell line
Runs (1)
Run Spots Bases Size (MB) Files Link
SRR22544228 25189302 2518930200 805.34 DDX42_DMSO.CLIP2.fastq.gz, SRR22544228, SRR22544228.lite SRA
SRX18508203 SRP411598 RIP-Seq SINGLE
GSM6793357: DDX42 SMInput treated with WX-02-23 (rep1); Homo sapiens; RIP-Seq
Sample: SRS15977290
BioProject: PRJNA909188
BioSample: SAMN32069681
Platform: ILLUMINA
Instrument: Illumina NovaSeq 6000
Organism: Homo sapiens
Sample attributes
source_name: HCT116 colon cancer cell line
cell type: HCT116, DDX42 HA-tagged
treatment: WX-02-23
clip antibody: none (input)
Original files (1)
HCT116 colon cancer cell line
Runs (1)
Run Spots Bases Size (MB) Files Link
SRR22544227 28309811 2830981100 900.77 SRR22544227.lite, SRR22544227, DDX42_WX-2-23.Input1.fastq.gz SRA
SRX18508204 SRP411598 RIP-Seq SINGLE
GSM6793358: DDX42 CLIP treated with WX-02-23 (rep1); Homo sapiens; RIP-Seq
Sample: SRS15977291
BioProject: PRJNA909188
BioSample: SAMN32069680
Platform: ILLUMINA
Instrument: Illumina NovaSeq 6000
Organism: Homo sapiens
Sample attributes
source_name: HCT116 colon cancer cell line
cell type: HCT116, DDX42 HA-tagged
treatment: WX-02-23
clip antibody: CST #3724S
Original files (1)
HCT116 colon cancer cell line
Runs (1)
Run Spots Bases Size (MB) Files Link
SRR22544226 20719180 2071918000 666.51 DDX42_WX-2-23.CLIP1.fastq.gz, SRR22544226, SRR22544226.lite SRA
SRX18508205 SRP411598 RIP-Seq SINGLE
GSM6793359: DDX42 SMInput treated with WX-02-23 (rep2); Homo sapiens; RIP-Seq
Sample: SRS15977292
BioProject: PRJNA909188
BioSample: SAMN32069679
Platform: ILLUMINA
Instrument: Illumina NovaSeq 6000
Organism: Homo sapiens
Sample attributes
source_name: HCT116 colon cancer cell line
cell type: HCT116, DDX42 HA-tagged
treatment: WX-02-23
clip antibody: none (input)
Original files (1)
HCT116 colon cancer cell line
Runs (1)
Run Spots Bases Size (MB) Files Link
SRR22544225 21026895 2102689500 675.87 DDX42_WX-2-23.Input2.fastq.gz, SRR22544225, SRR22544225.lite SRA
SRX18508206 SRP411598 RIP-Seq SINGLE
GSM6793360: DDX42 CLIP treated with WX-02-23 (rep2); Homo sapiens; RIP-Seq
Sample: SRS15977293
BioProject: PRJNA909188
BioSample: SAMN32069678
Platform: ILLUMINA
Instrument: Illumina NovaSeq 6000
Organism: Homo sapiens
Sample attributes
source_name: HCT116 colon cancer cell line
cell type: HCT116, DDX42 HA-tagged
treatment: WX-02-23
clip antibody: CST #3724S
Original files (1)
HCT116 colon cancer cell line
Runs (1)
Run Spots Bases Size (MB) Files Link
SRR22544224 28799800 2879980000 923.35 DDX42_WX-2-23.CLIP2.fastq.gz, SRR22544224, SRR22544224.lite SRA
SRX18508207 SRP411598 RIP-Seq SINGLE
GSM6793361: DDX42 SMInput treated with WX-02-43 (rep1); Homo sapiens; RIP-Seq
Sample: SRS15977294
BioProject: PRJNA909188
BioSample: SAMN32069677
Platform: ILLUMINA
Instrument: Illumina NovaSeq 6000
Organism: Homo sapiens
Sample attributes
source_name: HCT116 colon cancer cell line
cell type: HCT116, DDX42 HA-tagged
treatment: WX-02-43
clip antibody: none (input)
Original files (1)
HCT116 colon cancer cell line
Runs (1)
Run Spots Bases Size (MB) Files Link
SRR22544223 31693151 3169315100 1012.03 DDX42_WX-2-43.Input1.fastq.gz, SRR22544223, SRR22544223.lite SRA
SRX18508208 SRP411598 RIP-Seq SINGLE
GSM6793362: DDX42 CLIP treated with WX-02-43 (rep1); Homo sapiens; RIP-Seq
Sample: SRS15977295
BioProject: PRJNA909188
BioSample: SAMN32069676
Platform: ILLUMINA
Instrument: Illumina NovaSeq 6000
Organism: Homo sapiens
Sample attributes
source_name: HCT116 colon cancer cell line
cell type: HCT116, DDX42 HA-tagged
treatment: WX-02-43
clip antibody: CST #3724S
Original files (1)
HCT116 colon cancer cell line
Runs (1)
Run Spots Bases Size (MB) Files Link
SRR22544222 19152371 1915237100 624.68 DDX42_WX-2-43.CLIP1.fastq.gz, SRR22544222, SRR22544222.lite SRA
SRX18508209 SRP411598 RIP-Seq SINGLE
GSM6793363: DDX42 SMInput treated with WX-02-43 (rep2); Homo sapiens; RIP-Seq
Sample: SRS15977296
BioProject: PRJNA909188
BioSample: SAMN32069675
Platform: ILLUMINA
Instrument: Illumina NovaSeq 6000
Organism: Homo sapiens
Sample attributes
source_name: HCT116 colon cancer cell line
cell type: HCT116, DDX42 HA-tagged
treatment: WX-02-43
clip antibody: none (input)
Original files (1)
HCT116 colon cancer cell line
Runs (1)
Run Spots Bases Size (MB) Files Link
SRR22544221 27442284 2744228400 878.11 DDX42_WX-2-43.Input2.fastq.gz, SRR22544221, SRR22544221.lite SRA
SRX18508210 SRP411598 RIP-Seq SINGLE
GSM6793364: DDX42 CLIP treated with WX-02-43 (rep2); Homo sapiens; RIP-Seq
Sample: SRS15977297
BioProject: PRJNA909188
BioSample: SAMN32069674
Platform: ILLUMINA
Instrument: Illumina NovaSeq 6000
Organism: Homo sapiens
Sample attributes
source_name: HCT116 colon cancer cell line
cell type: HCT116, DDX42 HA-tagged
treatment: WX-02-43
clip antibody: CST #3724S
Original files (1)
HCT116 colon cancer cell line
Runs (1)
Run Spots Bases Size (MB) Files Link
SRR22544220 20382423 2038242300 660.85 DDX42_WX-2-43.CLIP2.fastq.gz, SRR22544220, SRR22544220.lite SRA
SRX18508211 SRP411598 RIP-Seq SINGLE
GSM6793365: DDX42 SMInput treated with PladB (rep1); Homo sapiens; RIP-Seq
Sample: SRS15977298
BioProject: PRJNA909188
BioSample: SAMN32069673
Platform: ILLUMINA
Instrument: Illumina NovaSeq 6000
Organism: Homo sapiens
Sample attributes
source_name: HCT116 colon cancer cell line
cell type: HCT116, DDX42 HA-tagged
treatment: Pladienolide B
clip antibody: none (input)
Original files (1)
HCT116 colon cancer cell line
Runs (1)
Run Spots Bases Size (MB) Files Link
SRR22544219 26200828 2620082800 840.7 DDX42_PladB.Input1.fastq.gz, SRR22544219, SRR22544219.lite SRA
SRX18508212 SRP411598 RIP-Seq SINGLE
GSM6793366: DDX42 CLIP treated with PladB (rep1); Homo sapiens; RIP-Seq
Sample: SRS15977299
BioProject: PRJNA909188
BioSample: SAMN32069672
Platform: ILLUMINA
Instrument: Illumina NovaSeq 6000
Organism: Homo sapiens
Sample attributes
source_name: HCT116 colon cancer cell line
cell type: HCT116, DDX42 HA-tagged
treatment: Pladienolide B
clip antibody: CST #3724S
Original files (1)
HCT116 colon cancer cell line
Runs (1)
Run Spots Bases Size (MB) Files Link
SRR22544218 25875349 2587534900 833.31 DDX42_PladB.CLIP1.fastq.gz, SRR22544218, SRR22544218.lite SRA
SRX18508213 SRP411598 RIP-Seq SINGLE
GSM6793367: DDX42 SMInput treated with PladB (rep2); Homo sapiens; RIP-Seq
Sample: SRS15977300
BioProject: PRJNA909188
BioSample: SAMN32069671
Platform: ILLUMINA
Instrument: Illumina NovaSeq 6000
Organism: Homo sapiens
Sample attributes
source_name: HCT116 colon cancer cell line
cell type: HCT116, DDX42 HA-tagged
treatment: Pladienolide B
clip antibody: none (input)
Original files (1)
HCT116 colon cancer cell line
Runs (1)
Run Spots Bases Size (MB) Files Link
SRR22544217 14957857 1495785700 485.9 DDX42_PladB.Input2.fastq.gz, SRR22544217, SRR22544217.lite SRA
SRX18508214 SRP411598 RIP-Seq SINGLE
GSM6793368: DDX42 CLIP treated with PladB (rep2); Homo sapiens; RIP-Seq
Sample: SRS15977301
BioProject: PRJNA909188
BioSample: SAMN32069670
Platform: ILLUMINA
Instrument: Illumina NovaSeq 6000
Organism: Homo sapiens
Sample attributes
source_name: HCT116 colon cancer cell line
cell type: HCT116, DDX42 HA-tagged
treatment: Pladienolide B
clip antibody: CST #3724S
Original files (1)
HCT116 colon cancer cell line
Runs (1)
Run Spots Bases Size (MB) Files Link
SRR22544216 29633022 2963302200 960.09 DDX42_PladB.CLIP2.fastq.gz, SRR22544216, SRR22544216.lite SRA

Linked Publications (2)

Proteomic discovery of chemical probes that perturb protein complexes in human cells.
Molecular cell · 2023
Flipper: An advanced framework for identifying differential RNA binding behavior with eCLIP data.
bioRxiv : the preprint server for biology · 2026

Data Files (16)

Accession File Name Stored Type Output Type Mapping Assembly Size Download
— DDX42_DMSO.CLIP1.fastq.gz RIP-Seq 1.6 GB link
— DDX42_DMSO.CLIP2.fastq.gz RIP-Seq 805.3 MB link
— DDX42_DMSO.Input1.fastq.gz RIP-Seq 1.0 GB link
— DDX42_DMSO.Input2.fastq.gz RIP-Seq 770.3 MB link
— DDX42_PladB.CLIP1.fastq.gz RIP-Seq 833.3 MB link
— DDX42_PladB.CLIP2.fastq.gz RIP-Seq 960.1 MB link
— DDX42_PladB.Input1.fastq.gz RIP-Seq 840.7 MB link
— DDX42_PladB.Input2.fastq.gz RIP-Seq 485.9 MB link
— DDX42_WX-2-23.CLIP1.fastq.gz RIP-Seq 666.5 MB link
— DDX42_WX-2-23.CLIP2.fastq.gz RIP-Seq 923.3 MB link
— DDX42_WX-2-23.Input2.fastq.gz RIP-Seq 675.9 MB link
— DDX42_WX-2-43.CLIP1.fastq.gz RIP-Seq 624.7 MB link
— DDX42_WX-2-43.CLIP2.fastq.gz RIP-Seq 660.8 MB link
— DDX42_WX-2-43.Input1.fastq.gz RIP-Seq 1012.0 MB link
— DDX42_WX-2-43.Input2.fastq.gz RIP-Seq 878.1 MB link
— SRR22544227.lite RIP-Seq 900.8 MB link