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GSE185373

GSE GEO
View on GEO Export SRA CSV

Function-first proteomic strategies for chemical probe discovery in human cells

Organism: Homo sapiens
Platform: GPL24676
Samples: 24
Experiment Types:
Expression profiling by high throughput sequencing
Submitted: Oct 05 2021
Last Updated: Apr 23 2023
Status: Public on Apr 19 2023
Contact: Simon,J,Hogg (AbbVie)

Relations

BioProject: https://www.ncbi.nlm.nih.gov/bioproject/PRJNA768835 SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRP340123

Summary

Transcriptional consequences of Pladienolide B, WX-02-23, and WX-02-43 treatment in 22Rv1 cells by RNA-sequencing

Overall Design

Treatment of 22Rv1 cells treated in biological triplicate with Pladienolide B, WX-02-23 (1µM and 5µM, respectively), WX-02-43, or DMSO vehicle control for 8 hours prior to RNA-sequencing. Treatment of 22Rv1 cells treated in biological triplicate with KB02 or KB05 (200 µM) for 1 hour followed by 2 hour recovery in fresh media prior to gene expression profiling by RNA-sequencing (RNA-seq).

Analysis (4 steps)

View Data Processing
Processing steps for GSE185373
  1. FASTQ files were first trimmed using Trim_galore (v0.6.4) to remove sequencing adapters and low quality (Q<15) reads.
  2. Trimmed sequencing reads were aligned to the human Hg19 reference genome (GENCODE, GRCh37.p13) using STAR (v2.7.5).
  3. SAM files were subsequently converted to BAM files, sorted, and indexed using samtools (v1.9).
  4. BAM files were used to generate bigwig files using bamCoverage (part of the Deeptools package; v3.3.1).

Supplementary Files (2)

GSE185373_RAW.tar Download
GSE185373_RNAseq_counts_raw.csv.gz Download
GEO Samples (24)
GSM5612127 GSM5612128 GSM5612129 GSM5612130 GSM5612131 GSM5612132 GSM5612133 GSM5612134 GSM5612135 GSM5612136 GSM5612137 GSM5612138 GSM5612139 GSM5612140 GSM5612141 GSM5686937 GSM5686938 GSM5686939 GSM5686940 GSM5686941 GSM5686942 GSM5686943 GSM5686944 GSM5686945

SRA Experiments (24) and Runs (24)

Total: 195162 MB
SRX12491366 SRP340123 RNA-Seq PAIRED
GSM5612127: Total_RNAseq_22Rv1_8hours_DMSO_Replicate1; Homo sapiens; RNA-Seq
Sample: SRS10454538
BioProject: PRJNA768835
BioSample: SAMN22064874
Platform: ILLUMINA
Instrument: Illumina NovaSeq 6000
Organism: Homo sapiens
Sample attributes
source_name: Prostate carcinoma
cell line: 22Rv1
time point: 8 hours
agent: DMSO
Original files (1)
Prostate carcinoma
Runs (1)
Run Spots Bases Size (MB) Files Link
SRR16207034 112492951 33747885300 11271.12 DMSO-1_R1_001.fastq.gz, DMSO-1_R2_001.fastq.gz, SRR16207034, SRR16207… SRA
SRX12491367 SRP340123 RNA-Seq PAIRED
GSM5612128: Total_RNAseq_22Rv1_8hours_DMSO_Replicate2; Homo sapiens; RNA-Seq
Sample: SRS10454539
BioProject: PRJNA768835
BioSample: SAMN22064876
Platform: ILLUMINA
Instrument: Illumina NovaSeq 6000
Organism: Homo sapiens
Sample attributes
source_name: Prostate carcinoma
cell line: 22Rv1
time point: 8 hours
agent: DMSO
Original files (1)
Prostate carcinoma
Runs (1)
Run Spots Bases Size (MB) Files Link
SRR16207035 112072755 33621826500 10944.85 DMSO-2_R1_001.fastq.gz, DMSO-2_R2_001.fastq.gz, SRR16207035, SRR16207… SRA
SRX12491368 SRP340123 RNA-Seq PAIRED
GSM5612129: Total_RNAseq_22Rv1_8hours_DMSO_Replicate3; Homo sapiens; RNA-Seq
Sample: SRS10454540
BioProject: PRJNA768835
BioSample: SAMN22064877
Platform: ILLUMINA
Instrument: Illumina NovaSeq 6000
Organism: Homo sapiens
Sample attributes
source_name: Prostate carcinoma
cell line: 22Rv1
time point: 8 hours
agent: DMSO
Original files (1)
Prostate carcinoma
Runs (1)
Run Spots Bases Size (MB) Files Link
SRR16207036 111729816 33518944800 10849.21 DMSO-3_R1_001.fastq.gz, DMSO-3_R2_001.fastq.gz, SRR16207036, SRR16207… SRA
SRX12491369 SRP340123 RNA-Seq PAIRED
GSM5612130: Total_RNAseq_22Rv1_8hours_PladienolideB_Replicate1; Homo sapiens; RNA-Seq
Sample: SRS10454541
BioProject: PRJNA768835
BioSample: SAMN22064879
Platform: ILLUMINA
Instrument: Illumina NovaSeq 6000
Organism: Homo sapiens
Sample attributes
source_name: Prostate carcinoma
cell line: 22Rv1
time point: 8 hours
agent: Pladienolide B
dose: 10nM
Original files (1)
Prostate carcinoma
Runs (1)
Run Spots Bases Size (MB) Files Link
SRR16207037 113404174 34021252200 10897.08 PB-10nM-1_R1_001.fastq.gz, PB-10nM-1_R2_001.fastq.gz, SRR16207037, SR… SRA
SRX12491370 SRP340123 RNA-Seq PAIRED
GSM5612131: Total_RNAseq_22Rv1_8hours_PladienolideB_Replicate2; Homo sapiens; RNA-Seq
Sample: SRS10454542
BioProject: PRJNA768835
BioSample: SAMN22064880
Platform: ILLUMINA
Instrument: Illumina NovaSeq 6000
Organism: Homo sapiens
Sample attributes
source_name: Prostate carcinoma
cell line: 22Rv1
time point: 8 hours
agent: Pladienolide B
dose: 10nM
Original files (1)
Prostate carcinoma
Runs (1)
Run Spots Bases Size (MB) Files Link
SRR16207038 119022727 35706818100 11958.21 PB-10nM-2_R1_001.fastq.gz, PB-10nM-2_R2_001.fastq.gz, SRR16207038, SR… SRA
SRX12491371 SRP340123 RNA-Seq PAIRED
GSM5612132: Total_RNAseq_22Rv1_8hours_PladienolideB_Replicate3; Homo sapiens; RNA-Seq
Sample: SRS10454543
BioProject: PRJNA768835
BioSample: SAMN22064881
Platform: ILLUMINA
Instrument: Illumina NovaSeq 6000
Organism: Homo sapiens
Sample attributes
source_name: Prostate carcinoma
cell line: 22Rv1
time point: 8 hours
agent: Pladienolide B
dose: 10nM
Original files (1)
Prostate carcinoma
Runs (1)
Run Spots Bases Size (MB) Files Link
SRR16207039 114193480 34258044000 11258.37 PB-10nM-3_R1_001.fastq.gz, PB-10nM-3_R2_001.fastq.gz, SRR16207039, SR… SRA
SRX12491372 SRP340123 RNA-Seq PAIRED
GSM5612133: Total_RNAseq_22Rv1_8hours_WX-02-23_1uM_Replicate1; Homo sapiens; RNA-Seq
Sample: SRS10454544
BioProject: PRJNA768835
BioSample: SAMN22064882
Platform: ILLUMINA
Instrument: Illumina NovaSeq 6000
Organism: Homo sapiens
Sample attributes
source_name: Prostate carcinoma
cell line: 22Rv1
time point: 8 hours
agent: WX-02-23
dose: 1microM
Original files (1)
Prostate carcinoma
Runs (1)
Run Spots Bases Size (MB) Files Link
SRR16207040 113089680 33926904000 10936.0 WX-02-23-1uM-1_R1_001.fastq.gz, WX-02-23-1uM-1_R2_001.fastq.gz, SRR16… SRA
SRX12491373 SRP340123 RNA-Seq PAIRED
GSM5612134: Total_RNAseq_22Rv1_8hours_WX-02-23_1uM_Replicate2; Homo sapiens; RNA-Seq
Sample: SRS10454545
BioProject: PRJNA768835
BioSample: SAMN22064883
Platform: ILLUMINA
Instrument: Illumina NovaSeq 6000
Organism: Homo sapiens
Sample attributes
source_name: Prostate carcinoma
cell line: 22Rv1
time point: 8 hours
agent: WX-02-23
dose: 1microM
Original files (1)
Prostate carcinoma
Runs (1)
Run Spots Bases Size (MB) Files Link
SRR16207041 116767612 35030283600 12745.38 WX-02-23-1uM-2_R1_001.fastq.gz, WX-02-23-1uM-2_R2_001.fastq.gz, SRR16… SRA
SRX12491374 SRP340123 RNA-Seq PAIRED
GSM5612135: Total_RNAseq_22Rv1_8hours_WX-02-23_1uM_Replicate3; Homo sapiens; RNA-Seq
Sample: SRS10454546
BioProject: PRJNA768835
BioSample: SAMN22064884
Platform: ILLUMINA
Instrument: Illumina NovaSeq 6000
Organism: Homo sapiens
Sample attributes
source_name: Prostate carcinoma
cell line: 22Rv1
time point: 8 hours
agent: WX-02-23
dose: 1microM
Original files (1)
Prostate carcinoma
Runs (1)
Run Spots Bases Size (MB) Files Link
SRR16207042 114982559 34494767700 11951.4 WX-02-23-1uM-3_R1_001.fastq.gz, WX-02-23-1uM-3_R2_001.fastq.gz, SRR16… SRA
SRX12491375 SRP340123 RNA-Seq PAIRED
GSM5612136: Total_RNAseq_22Rv1_8hours_WX-02-23_5uM_Replicate1; Homo sapiens; RNA-Seq
Sample: SRS10454547
BioProject: PRJNA768835
BioSample: SAMN22064885
Platform: ILLUMINA
Instrument: Illumina NovaSeq 6000
Organism: Homo sapiens
Sample attributes
source_name: Prostate carcinoma
cell line: 22Rv1
time point: 8 hours
agent: WX-02-23
dose: 5microM
Original files (1)
Prostate carcinoma
Runs (1)
Run Spots Bases Size (MB) Files Link
SRR16207043 114409368 34322810400 11689.94 WX-02-23-5uM-1_R1_001.fastq.gz, WX-02-23-5uM-1_R2_001.fastq.gz, SRR16… SRA
SRX12491376 SRP340123 RNA-Seq PAIRED
GSM5612137: Total_RNAseq_22Rv1_8hours_WX-02-23_5uM_Replicate2; Homo sapiens; RNA-Seq
Sample: SRS10454548
BioProject: PRJNA768835
BioSample: SAMN22064886
Platform: ILLUMINA
Instrument: Illumina NovaSeq 6000
Organism: Homo sapiens
Sample attributes
source_name: Prostate carcinoma
cell line: 22Rv1
time point: 8 hours
agent: WX-02-23
dose: 5microM
Original files (1)
Prostate carcinoma
Runs (1)
Run Spots Bases Size (MB) Files Link
SRR16207044 115102694 34530808200 11150.1 WX-02-23-5uM-2_R1_001.fastq.gz, WX-02-23-5uM-2_R2_001.fastq.gz, SRR16… SRA
SRX12491377 SRP340123 RNA-Seq PAIRED
GSM5612138: Total_RNAseq_22Rv1_8hours_WX-02-23_5uM_Replicate3; Homo sapiens; RNA-Seq
Sample: SRS10454549
BioProject: PRJNA768835
BioSample: SAMN22064887
Platform: ILLUMINA
Instrument: Illumina NovaSeq 6000
Organism: Homo sapiens
Sample attributes
source_name: Prostate carcinoma
cell line: 22Rv1
time point: 8 hours
agent: WX-02-23
dose: 5microM
Original files (1)
Prostate carcinoma
Runs (1)
Run Spots Bases Size (MB) Files Link
SRR16207045 116084203 34825260900 11694.97 WX-02-23-5uM-3_R1_001.fastq.gz, WX-02-23-5uM-3_R2_001.fastq.gz, SRR16… SRA
SRX12491378 SRP340123 RNA-Seq PAIRED
GSM5612139: Total_RNAseq_22Rv1_8hours_WX-02-43_5uM_Replicate1; Homo sapiens; RNA-Seq
Sample: SRS10454550
BioProject: PRJNA768835
BioSample: SAMN22064888
Platform: ILLUMINA
Instrument: Illumina NovaSeq 6000
Organism: Homo sapiens
Sample attributes
source_name: Prostate carcinoma
cell line: 22Rv1
time point: 8 hours
agent: WX-02-43
dose: 5microM
Original files (1)
Prostate carcinoma
Runs (1)
Run Spots Bases Size (MB) Files Link
SRR16207046 123221943 36966582900 12938.66 WX-02-43-5uM-1_R1_001.fastq.gz, WX-02-43-5uM-1_R2_001.fastq.gz, SRR16… SRA
SRX12491379 SRP340123 RNA-Seq PAIRED
GSM5612140: Total_RNAseq_22Rv1_8hours_WX-02-43_5uM_Replicate2; Homo sapiens; RNA-Seq
Sample: SRS10454551
BioProject: PRJNA768835
BioSample: SAMN22064889
Platform: ILLUMINA
Instrument: Illumina NovaSeq 6000
Organism: Homo sapiens
Sample attributes
source_name: Prostate carcinoma
cell line: 22Rv1
time point: 8 hours
agent: WX-02-43
dose: 5microM
Original files (1)
Prostate carcinoma
Runs (1)
Run Spots Bases Size (MB) Files Link
SRR16207047 116583208 34974962400 11885.65 WX-02-43-5uM-2_R1_001.fastq.gz, WX-02-43-5uM-2_R2_001.fastq.gz, SRR16… SRA
SRX12491380 SRP340123 RNA-Seq PAIRED
GSM5612141: Total_RNAseq_22Rv1_8hours_WX-02-43_5uM_Replicate3; Homo sapiens; RNA-Seq
Sample: SRS10454552
BioProject: PRJNA768835
BioSample: SAMN22064890
Platform: ILLUMINA
Instrument: Illumina NovaSeq 6000
Organism: Homo sapiens
Sample attributes
source_name: Prostate carcinoma
cell line: 22Rv1
time point: 8 hours
agent: WX-02-43
dose: 5microM
Original files (1)
Prostate carcinoma
Runs (1)
Run Spots Bases Size (MB) Files Link
SRR16207048 120981980 36294594000 12469.05 WX-02-43-5uM-3_R1_001.fastq.gz, WX-02-43-5uM-3_R2_001.fastq.gz, SRR16… SRA
SRX13111832 SRP340123 RNA-Seq PAIRED
GSM5686937: RNAseq_22Rv1_3hours_DMSO_Replicate_1; Homo sapiens; RNA-Seq
Sample: SRS11047128
BioProject: PRJNA768835
BioSample: SAMN23070941
Platform: ILLUMINA
Instrument: Illumina NovaSeq 6000
Organism: Homo sapiens
Sample attributes
source_name: Prostate carcinoma
cell line: 22Rv1
timepoint: 3 hours
agent: DMSO
Original files (1)
Prostate carcinoma
Runs (1)
Run Spots Bases Size (MB) Files Link
SRR16919523 23745330 7123599000 2292.14 DMSO-2h-1_R1_001.fastq.gz, DMSO-2h-1_R2_001.fastq.gz, SRR16919523, SR… SRA
SRX13111833 SRP340123 RNA-Seq PAIRED
GSM5686938: RNAseq_22Rv1_3hours_DMSO_Replicate_2; Homo sapiens; RNA-Seq
Sample: SRS11047130
BioProject: PRJNA768835
BioSample: SAMN23070942
Platform: ILLUMINA
Instrument: Illumina NovaSeq 6000
Organism: Homo sapiens
Sample attributes
source_name: Prostate carcinoma
cell line: 22Rv1
timepoint: 3 hours
agent: DMSO
Original files (1)
Prostate carcinoma
Runs (1)
Run Spots Bases Size (MB) Files Link
SRR16919524 24842473 7452741900 2397.04 DMSO-2h-2_R1_001.fastq.gz, DMSO-2h-2_R2_001.fastq.gz, SRR16919524, SR… SRA
SRX13111834 SRP340123 RNA-Seq PAIRED
GSM5686939: RNAseq_22Rv1_3hours_DMSO_Replicate_3; Homo sapiens; RNA-Seq
Sample: SRS11047131
BioProject: PRJNA768835
BioSample: SAMN23070944
Platform: ILLUMINA
Instrument: Illumina NovaSeq 6000
Organism: Homo sapiens
Sample attributes
source_name: Prostate carcinoma
cell line: 22Rv1
timepoint: 3 hours
agent: DMSO
Original files (1)
Prostate carcinoma
Runs (1)
Run Spots Bases Size (MB) Files Link
SRR16919525 22052759 6615827700 2129.15 DMSO-2h-3_R1_001.fastq.gz, DMSO-2h-3_R2_001.fastq.gz, SRR16919525, SR… SRA
SRX13111835 SRP340123 RNA-Seq PAIRED
GSM5686940: RNAseq_22Rv1_3hours_KB02_Replicate_1; Homo sapiens; RNA-Seq
Sample: SRS11047132
BioProject: PRJNA768835
BioSample: SAMN23070945
Platform: ILLUMINA
Instrument: Illumina NovaSeq 6000
Organism: Homo sapiens
Sample attributes
source_name: Prostate carcinoma
cell line: 22Rv1
timepoint: 3 hours
agent: KB02
dose: 200microM
Original files (1)
Prostate carcinoma
Runs (1)
Run Spots Bases Size (MB) Files Link
SRR16919526 26246831 7874049300 2588.02 KB02-2h-1_R1_001.fastq.gz, KB02-2h-1_R2_001.fastq.gz, SRR16919526, SR… SRA
SRX13111836 SRP340123 RNA-Seq PAIRED
GSM5686941: RNAseq_22Rv1_3hours_KB02_Replicate_2; Homo sapiens; RNA-Seq
Sample: SRS11047133
BioProject: PRJNA768835
BioSample: SAMN23070946
Platform: ILLUMINA
Instrument: Illumina NovaSeq 6000
Organism: Homo sapiens
Sample attributes
source_name: Prostate carcinoma
cell line: 22Rv1
timepoint: 3 hours
agent: KB02
dose: 200microM
Original files (1)
Prostate carcinoma
Runs (1)
Run Spots Bases Size (MB) Files Link
SRR16919527 25943531 7783059300 2518.67 KB02-2h-2_R1_001.fastq.gz, KB02-2h-2_R2_001.fastq.gz, SRR16919527, SR… SRA
SRX13111837 SRP340123 RNA-Seq PAIRED
GSM5686942: RNAseq_22Rv1_3hours_KB02_Replicate_3; Homo sapiens; RNA-Seq
Sample: SRS11047134
BioProject: PRJNA768835
BioSample: SAMN23070948
Platform: ILLUMINA
Instrument: Illumina NovaSeq 6000
Organism: Homo sapiens
Sample attributes
source_name: Prostate carcinoma
cell line: 22Rv1
timepoint: 3 hours
agent: KB02
dose: 200microM
Original files (1)
Prostate carcinoma
Runs (1)
Run Spots Bases Size (MB) Files Link
SRR16919528 21570910 6471273000 2078.62 KB02-2h-3_R1_001.fastq.gz, KB02-2h-3_R2_001.fastq.gz, SRR16919528, SR… SRA
SRX13111838 SRP340123 RNA-Seq PAIRED
GSM5686943: RNAseq_22Rv1_3hours_KB05_Replicate_1; Homo sapiens; RNA-Seq
Sample: SRS11047135
BioProject: PRJNA768835
BioSample: SAMN23070949
Platform: ILLUMINA
Instrument: Illumina NovaSeq 6000
Organism: Homo sapiens
Sample attributes
source_name: Prostate carcinoma
cell line: 22Rv1
timepoint: 3 hours
agent: KB05
dose: 200microM
Original files (1)
Prostate carcinoma
Runs (1)
Run Spots Bases Size (MB) Files Link
SRR16919529 25648898 7694669400 2470.06 KB05-2h-1_R1_001.fastq.gz, KB05-2h-1_R2_001.fastq.gz, SRR16919529, SR… SRA
SRX13111839 SRP340123 RNA-Seq PAIRED
GSM5686944: RNAseq_22Rv1_3hours_KB05_Replicate_2; Homo sapiens; RNA-Seq
Sample: SRS11047136
BioProject: PRJNA768835
BioSample: SAMN23070950
Platform: ILLUMINA
Instrument: Illumina NovaSeq 6000
Organism: Homo sapiens
Sample attributes
source_name: Prostate carcinoma
cell line: 22Rv1
timepoint: 3 hours
agent: KB05
dose: 200microM
Original files (1)
Prostate carcinoma
Runs (1)
Run Spots Bases Size (MB) Files Link
SRR16919530 19234509 5770352700 1855.33 KB05-2h-2_R1_001.fastq.gz, KB05-2h-2_R2_001.fastq.gz, SRR16919530, SR… SRA
SRX13111840 SRP340123 RNA-Seq PAIRED
GSM5686945: RNAseq_22Rv1_3hours_KB05_Replicate_3; Homo sapiens; RNA-Seq
Sample: SRS11047137
BioProject: PRJNA768835
BioSample: SAMN23070952
Platform: ILLUMINA
Instrument: Illumina NovaSeq 6000
Organism: Homo sapiens
Sample attributes
source_name: Prostate carcinoma
cell line: 22Rv1
timepoint: 3 hours
agent: KB05
dose: 200microM
Original files (1)
Prostate carcinoma
Runs (1)
Run Spots Bases Size (MB) Files Link
SRR16919531 22788578 6836573400 2192.85 KB05-2h-3_R1_001.fastq.gz, KB05-2h-3_R2_001.fastq.gz, SRR16919531, SR… SRA

Linked Publications (1)

Proteomic discovery of chemical probes that perturb protein complexes in human cells.
Molecular cell · 2023

Data Files (24)

Accession File Name Stored Type Output Type Mapping Assembly Size Download
— DMSO-1_R1_001.fastq.gz RNA-Seq 11.0 GB link
— DMSO-2h-1_R1_001.fastq.gz RNA-Seq 2.2 GB link
— DMSO-2h-2_R1_001.fastq.gz RNA-Seq 2.3 GB link
— DMSO-2h-3_R1_001.fastq.gz RNA-Seq 2.1 GB link
— DMSO-2_R1_001.fastq.gz RNA-Seq 10.7 GB link
— DMSO-3_R1_001.fastq.gz RNA-Seq 10.6 GB link
— KB02-2h-1_R1_001.fastq.gz RNA-Seq 2.5 GB link
— KB02-2h-2_R1_001.fastq.gz RNA-Seq 2.5 GB link
— KB02-2h-3_R1_001.fastq.gz RNA-Seq 2.0 GB link
— KB05-2h-1_R1_001.fastq.gz RNA-Seq 2.4 GB link
— KB05-2h-2_R1_001.fastq.gz RNA-Seq 1.8 GB link
— KB05-2h-3_R1_001.fastq.gz RNA-Seq 2.1 GB link
— PB-10nM-1_R1_001.fastq.gz RNA-Seq 10.6 GB link
— PB-10nM-2_R1_001.fastq.gz RNA-Seq 11.7 GB link
— PB-10nM-3_R1_001.fastq.gz RNA-Seq 11.0 GB link
— WX-02-23-1uM-1_R1_001.fastq.gz RNA-Seq 10.7 GB link
— WX-02-23-1uM-2_R1_001.fastq.gz RNA-Seq 12.4 GB link
— WX-02-23-1uM-3_R1_001.fastq.gz RNA-Seq 11.7 GB link
— WX-02-23-5uM-1_R1_001.fastq.gz RNA-Seq 11.4 GB link
— WX-02-23-5uM-2_R1_001.fastq.gz RNA-Seq 10.9 GB link
— WX-02-23-5uM-3_R1_001.fastq.gz RNA-Seq 11.4 GB link
— WX-02-43-5uM-1_R1_001.fastq.gz RNA-Seq 12.6 GB link
— WX-02-43-5uM-2_R1_001.fastq.gz RNA-Seq 11.6 GB link
— WX-02-43-5uM-3_R1_001.fastq.gz RNA-Seq 12.2 GB link