GSE232598

GSE GEO

View on GEO Export SRA CSV

Systematic identification of RNA-binding proteins and tethered domains that activate exon splicing inclusion [RNA-seq]

Organism: Homo sapiens

Platform: GPL24676

Samples: 15

Experiment Types:

Expression profiling by high throughput sequencing

Submitted: May 16 2023

Last Updated: Oct 08 2024

Status: Public on Sep 25 2023

Contact: Brian,,Yee (UCSD)

Relations

SubSeries of: GSE232599 BioProject: https://www.ncbi.nlm.nih.gov/bioproject/PRJNA972981

Summary

RNA-binding proteins (RBPs) modulate alternative splicing outcomes to determine isoform expression and cellular survival. To identify RBPs that directly drive alternative exon inclusion, we evaluated 718 human RBPs with tethered function luciferase-based splicing reporter assays to identify 58 candidates, including known splicing factors such as RBFOX and serine-arginine proteins. We performed enhanced CLIP, RNA-seq, and affinity purification-mass spectrometry to investigate a subset of the 11 candidates with no prior association with splicing. Integrative analysis of these assays indicated the surprising roles of TRNAU1AP, SCAF8, and RTCA in modulating hundreds of endogenous splicing events. We also leveraged our tethering assays and top candidates to identify potent and compact exon inclusion activation domains for splicing modulation applications. Using identified domains, we engineered programmable fusion proteins which outperformed current artificial splicing factors at manipulating inclusion of reporter and endogenous exons. Altogether, our tethering approach characterized the ability of RBPs to induce exon inclusion and yielded new molecular parts for programmable splicing control.

Overall Design

Differential splicing and expression analysis of RNA-seq data for HEK293T cells and its KD derivatives (shTRNAU1AP, shSTAU2, shSCAF8, shRTCA).

Analysis (6 steps)

View Data Processing

Processing steps for GSE232598

Reads were mapped using STAR 2.7.6a
Read count extraction was performed using featureCounts from the Subread package.
Results were sorted into counts matrices
TPM was calculated manually from counts matrix
Differential splicing analysis was performed on STAR-aligned reads using rMATS 4.0.2.
For each condition, shRNA knockdown samples represent SAMPLE_1, while non-targeting controls (shNT_1, shNT_2, and shNT_3) represent SAMPLE_2.

Supplementary Files (8)

GSE232598_shRTCA_SE.MATS.JC.txt.gz Download

GSE232598_shRTCA_TPM.csv.gz Download

GSE232598_shSCAF8_SE.MATS.JC.txt.gz Download

GSE232598_shSCAF8_TPM.csv.gz Download

GSE232598_shSTAU2_SE.MATS.JC.txt.gz Download

GSE232598_shSTAU2_TPM.csv.gz Download

GSE232598_shTRNAU1AP_SE.MATS.JC.txt.gz Download

GSE232598_shTRNAU1AP_TPM.csv.gz Download

GEO Samples (15)

GSM7359797 GSM7359798 GSM7359799 GSM7359800 GSM7359801 GSM7359802 GSM7359803 GSM7359804 GSM7359805 GSM7359806 GSM7359807 GSM7359808 GSM7359812 GSM7359813 GSM7359814

Dataset Citations (1)

Large-scale evaluation of the ability of RNA-binding proteins to activate exon inclusion.

PMID 38168984 · 2024 · Nature biotechnology

Jonathan C Schmok, Manya Jain, Lena A Street, Alex T Tankka, Danielle Schafer, Hsuan-Lin Her, Sara Elmsaouri, Maya L Gosztyla, Evan A Boyle, Pratibha Jagannatha, En-Ching Luo, Ester J Kwon, Marko Jovanovic, Gene W Yeo

SRA Experiments (15) and Runs (15)

Total: 78357 MB

SRX20362953 SRP437932 RNA-Seq PAIRED

GSM7359797: HEK293T cells, shTRNAU1AP, Rep1; Homo sapiens; RNA-Seq

Sample: SRS17679879

BioProject: PRJNA972981

BioSample: SAMN35102988

Platform: ILLUMINA

Instrument: Illumina NovaSeq 6000

Organism: Homo sapiens

Sample attributes

source_name: HEK293T

cell line: HEK293T

cell type: Human Embryonic Kidney

genotype: TRNAU1AP knockdown

geo_loc_name: missing

collection_date: missing

Original files (1)

HEK293T

Runs (1)

Run	Spots	Bases	Size (MB)	Files	Link
SRR24579608	91157025	18413719050	5746.38	shTRNAU1AP_1_R1.fastq.gz, shTRNAU1AP_1_R2.fastq.gz, SRR24579608, SRR2…	SRA

SRX20362954 SRP437932 RNA-Seq PAIRED

GSM7359798: HEK293T cells, shTRNAU1AP, Rep2; Homo sapiens; RNA-Seq

Sample: SRS17679880

BioProject: PRJNA972981

BioSample: SAMN35102987

Platform: ILLUMINA

Instrument: Illumina NovaSeq 6000

Organism: Homo sapiens

Sample attributes

source_name: HEK293T

cell line: HEK293T

cell type: Human Embryonic Kidney

genotype: TRNAU1AP knockdown

geo_loc_name: missing

collection_date: missing

Original files (1)

HEK293T

Runs (1)

Run	Spots	Bases	Size (MB)	Files	Link
SRR24579607	78348721	15826441642	4936.93	shTRNAU1AP_2_R1.fastq.gz, shTRNAU1AP_2_R2.fastq.gz, SRR24579607, SRR2…	SRA

SRX20362955 SRP437932 RNA-Seq PAIRED

GSM7359799: HEK293T cells, shTRNAU1AP, Rep3; Homo sapiens; RNA-Seq

Sample: SRS17679881

BioProject: PRJNA972981

BioSample: SAMN35102986

Platform: ILLUMINA

Instrument: Illumina NovaSeq 6000

Organism: Homo sapiens

Sample attributes

source_name: HEK293T

cell line: HEK293T

cell type: Human Embryonic Kidney

genotype: TRNAU1AP knockdown

geo_loc_name: missing

collection_date: missing

Original files (1)

HEK293T

Runs (1)

Run	Spots	Bases	Size (MB)	Files	Link
SRR24579606	91812557	18546136514	5764.65	shTRNAU1AP_3_R1.fastq.gz, shTRNAU1AP_3_R2.fastq.gz, SRR24579606, SRR2…	SRA

SRX20362956 SRP437932 RNA-Seq PAIRED

GSM7359800: HEK293T cells, shRTCA, Rep1; Homo sapiens; RNA-Seq

Sample: SRS17679882

BioProject: PRJNA972981

BioSample: SAMN35102985

Platform: ILLUMINA

Instrument: Illumina NovaSeq 6000

Organism: Homo sapiens

Sample attributes

source_name: HEK293T

cell line: HEK293T

cell type: Human Embryonic Kidney

genotype: RTCA knockdown

geo_loc_name: missing

collection_date: missing

Original files (1)

HEK293T

Runs (1)

Run	Spots	Bases	Size (MB)	Files	Link
SRR24579605	87050789	17584259378	5461.51	shRTCA_1_R1.fastq.gz, shRTCA_1_R2.fastq.gz, SRR24579605, SRR24579605.…	SRA

SRX20362957 SRP437932 RNA-Seq PAIRED

GSM7359801: HEK293T cells, shRTCA, Rep2; Homo sapiens; RNA-Seq

Sample: SRS17679883

BioProject: PRJNA972981

BioSample: SAMN35102984

Platform: ILLUMINA

Instrument: Illumina NovaSeq 6000

Organism: Homo sapiens

Sample attributes

source_name: HEK293T

cell line: HEK293T

cell type: Human Embryonic Kidney

genotype: RTCA knockdown

geo_loc_name: missing

collection_date: missing

Original files (1)

HEK293T

Runs (1)

Run	Spots	Bases	Size (MB)	Files	Link
SRR24579604	77420959	15639033718	4856.08	shRTCA_2_R1.fastq.gz, shRTCA_2_R2.fastq.gz, SRR24579604, SRR24579604.…	SRA

SRX20362958 SRP437932 RNA-Seq PAIRED

GSM7359802: HEK293T cells, shRTCA, Rep3; Homo sapiens; RNA-Seq

Sample: SRS17679884

BioProject: PRJNA972981

BioSample: SAMN35102983

Platform: ILLUMINA

Instrument: Illumina NovaSeq 6000

Organism: Homo sapiens

Sample attributes

source_name: HEK293T

cell line: HEK293T

cell type: Human Embryonic Kidney

genotype: RTCA knockdown

geo_loc_name: missing

collection_date: missing

Original files (1)

HEK293T

Runs (1)

Run	Spots	Bases	Size (MB)	Files	Link
SRR24579603	80713852	16304198104	5076.04	shRTCA_3_R1.fastq.gz, shRTCA_3_R2.fastq.gz, SRR24579603, SRR24579603.…	SRA

SRX20362959 SRP437932 RNA-Seq PAIRED

GSM7359803: HEK293T cells, shSCAF8, Rep1; Homo sapiens; RNA-Seq

Sample: SRS17679885

BioProject: PRJNA972981

BioSample: SAMN35102982

Platform: ILLUMINA

Instrument: Illumina NovaSeq 6000

Organism: Homo sapiens

Sample attributes

source_name: HEK293T

cell line: HEK293T

cell type: Human Embryonic Kidney

genotype: SCAF8 knockdown

geo_loc_name: missing

collection_date: missing

Original files (1)

HEK293T

Runs (1)

Run	Spots	Bases	Size (MB)	Files	Link
SRR24579602	78288004	15814176808	4985.46	shSCAF8_1_R1.fastq.gz, shSCAF8_1_R2.fastq.gz, SRR24579602, SRR2457960…	SRA

SRX20362960 SRP437932 RNA-Seq PAIRED

GSM7359804: HEK293T cells, shSCAF8, Rep2; Homo sapiens; RNA-Seq

Sample: SRS17679886

BioProject: PRJNA972981

BioSample: SAMN35102981

Platform: ILLUMINA

Instrument: Illumina NovaSeq 6000

Organism: Homo sapiens

Sample attributes

source_name: HEK293T

cell line: HEK293T

cell type: Human Embryonic Kidney

genotype: SCAF8 knockdown

geo_loc_name: missing

collection_date: missing

Original files (1)

HEK293T

Runs (1)

Run	Spots	Bases	Size (MB)	Files	Link
SRR24579601	85933111	17358488422	5444.41	shSCAF8_2_R1.fastq.gz, shSCAF8_2_R2.fastq.gz, SRR24579601, SRR2457960…	SRA

SRX20362961 SRP437932 RNA-Seq PAIRED

GSM7359805: HEK293T cells, shSCAF8, Rep3; Homo sapiens; RNA-Seq

Sample: SRS17679887

BioProject: PRJNA972981

BioSample: SAMN35102980

Platform: ILLUMINA

Instrument: Illumina NovaSeq 6000

Organism: Homo sapiens

Sample attributes

source_name: HEK293T

cell line: HEK293T

cell type: Human Embryonic Kidney

genotype: SCAF8 knockdown

geo_loc_name: missing

collection_date: missing

Original files (1)

HEK293T

Runs (1)

Run	Spots	Bases	Size (MB)	Files	Link
SRR24579600	78584104	15873989008	4958.5	shSCAF8_3_R1.fastq.gz, shSCAF8_3_R2.fastq.gz, SRR24579600, SRR2457960…	SRA

SRX20362962 SRP437932 RNA-Seq PAIRED

GSM7359806: HEK293T cells, shSTAU2, Rep1; Homo sapiens; RNA-Seq

Sample: SRS17679888

BioProject: PRJNA972981

BioSample: SAMN35102979

Platform: ILLUMINA

Instrument: Illumina NovaSeq 6000

Organism: Homo sapiens

Sample attributes

source_name: HEK293T

cell line: HEK293T

cell type: Human Embryonic Kidney

genotype: STAU2 knockdown

geo_loc_name: missing

collection_date: missing

Original files (1)

HEK293T

Runs (1)

Run	Spots	Bases	Size (MB)	Files	Link
SRR24579599	76972953	15548536506	4876.49	shSTAU2_1_R1.fastq.gz, shSTAU2_1_R2.fastq.gz, SRR24579599, SRR2457959…	SRA

SRX20362963 SRP437932 RNA-Seq PAIRED

GSM7359807: HEK293T cells, shSTAU2, Rep2; Homo sapiens; RNA-Seq

Sample: SRS17679889

BioProject: PRJNA972981

BioSample: SAMN35102978

Platform: ILLUMINA

Instrument: Illumina NovaSeq 6000

Organism: Homo sapiens

Sample attributes

source_name: HEK293T

cell line: HEK293T

cell type: Human Embryonic Kidney

genotype: STAU2 knockdown

geo_loc_name: missing

collection_date: missing

Original files (1)

HEK293T

Runs (1)

Run	Spots	Bases	Size (MB)	Files	Link
SRR24579598	70862341	14314192882	4674.48	shSTAU2_2_R1.fastq.gz, shSTAU2_2_R2.fastq.gz, SRR24579598, SRR2457959…	SRA

SRX20362964 SRP437932 RNA-Seq PAIRED

GSM7359808: HEK293T cells, shSTAU2, Rep3; Homo sapiens; RNA-Seq

Sample: SRS17679890

BioProject: PRJNA972981

BioSample: SAMN35102977

Platform: ILLUMINA

Instrument: Illumina NovaSeq 6000

Organism: Homo sapiens

Sample attributes

source_name: HEK293T

cell line: HEK293T

cell type: Human Embryonic Kidney

genotype: STAU2 knockdown

geo_loc_name: missing

collection_date: missing

Original files (1)

HEK293T

Runs (1)

Run	Spots	Bases	Size (MB)	Files	Link
SRR24579597	74810552	15111731504	4765.86	shSTAU2_3_R1.fastq.gz, shSTAU2_3_R2.fastq.gz, SRR24579597, SRR2457959…	SRA

SRX20362968 SRP437932 RNA-Seq PAIRED

GSM7359812: HEK293T cells, shNT, Rep1; Homo sapiens; RNA-Seq

Sample: SRS17679895

BioProject: PRJNA972981

BioSample: SAMN35102973

Platform: ILLUMINA

Instrument: Illumina NovaSeq 6000

Organism: Homo sapiens

Sample attributes

source_name: HEK293T

cell line: HEK293T

cell type: Human Embryonic Kidney

genotype: Non-targeting shRNA

geo_loc_name: missing

collection_date: missing

Original files (1)

HEK293T

Runs (1)

Run	Spots	Bases	Size (MB)	Files	Link
SRR24579593	80705007	16302411414	5091.77	shNT_1_R1.fastq.gz, shNT_1_R2.fastq.gz, SRR24579593, SRR24579593.lite	SRA

SRX20362969 SRP437932 RNA-Seq PAIRED

GSM7359813: HEK293T cells, shNT, Rep2; Homo sapiens; RNA-Seq

Sample: SRS17679894

BioProject: PRJNA972981

BioSample: SAMN35102972

Platform: ILLUMINA

Instrument: Illumina NovaSeq 6000

Organism: Homo sapiens

Sample attributes

source_name: HEK293T

cell line: HEK293T

cell type: Human Embryonic Kidney

genotype: Non-targeting shRNA

geo_loc_name: missing

collection_date: missing

Original files (1)

HEK293T

Runs (1)

Run	Spots	Bases	Size (MB)	Files	Link
SRR24579592	84048227	16977741854	5283.05	shNT_2_R1.fastq.gz, shNT_2_R2.fastq.gz, SRR24579592, SRR24579592.lite	SRA

SRX20362970 SRP437932 RNA-Seq PAIRED

GSM7359814: HEK293T cells, shNT, Rep3; Homo sapiens; RNA-Seq

Sample: SRS17679896

BioProject: PRJNA972981

BioSample: SAMN35102971

Platform: ILLUMINA

Instrument: Illumina NovaSeq 6000

Organism: Homo sapiens

Sample attributes

source_name: HEK293T

cell line: HEK293T

cell type: Human Embryonic Kidney

genotype: Non-targeting shRNA

geo_loc_name: missing

collection_date: missing

Original files (1)

HEK293T

Runs (1)

Run	Spots	Bases	Size (MB)	Files	Link
SRR24579591	101900186	20583837572	6434.94	shNT_3_R1.fastq.gz, shNT_3_R2.fastq.gz, SRR24579591, SRR24579591.lite	SRA

Linked Publications (1)

Large-scale evaluation of the ability of RNA-binding proteins to activate exon inclusion.

Nature biotechnology · 2024

Data Files (30)

Accession	File Name	Stored Type	Size	Download
—	shNT_1_R1.fastq.gz	RNA-Seq	5.0 GB	link
—	shNT_1_R1.fastq.gz	RNA-Seq	5.0 GB	link
—	shNT_2_R1.fastq.gz	RNA-Seq	5.2 GB	link
—	shNT_2_R1.fastq.gz	RNA-Seq	5.2 GB	link
—	shNT_3_R1.fastq.gz	RNA-Seq	6.3 GB	link
—	shNT_3_R1.fastq.gz	RNA-Seq	6.3 GB	link
—	shRTCA_1_R1.fastq.gz	RNA-Seq	5.3 GB	link
—	shRTCA_1_R1.fastq.gz	RNA-Seq	5.3 GB	link
—	shRTCA_2_R1.fastq.gz	RNA-Seq	4.7 GB	link
—	shRTCA_2_R1.fastq.gz	RNA-Seq	4.7 GB	link
—	shRTCA_3_R1.fastq.gz	RNA-Seq	5.0 GB	link
—	shRTCA_3_R1.fastq.gz	RNA-Seq	5.0 GB	link
—	shSCAF8_1_R1.fastq.gz	RNA-Seq	4.9 GB	link
—	shSCAF8_1_R1.fastq.gz	RNA-Seq	4.9 GB	link
—	shSCAF8_2_R1.fastq.gz	RNA-Seq	5.3 GB	link
—	shSCAF8_2_R1.fastq.gz	RNA-Seq	5.3 GB	link
—	shSCAF8_3_R1.fastq.gz	RNA-Seq	4.8 GB	link
—	shSCAF8_3_R1.fastq.gz	RNA-Seq	4.8 GB	link
—	shSTAU2_1_R1.fastq.gz	RNA-Seq	4.8 GB	link
—	shSTAU2_1_R1.fastq.gz	RNA-Seq	4.8 GB	link
—	shSTAU2_2_R1.fastq.gz	RNA-Seq	4.6 GB	link
—	shSTAU2_2_R1.fastq.gz	RNA-Seq	4.6 GB	link
—	shSTAU2_3_R1.fastq.gz	RNA-Seq	4.7 GB	link
—	shSTAU2_3_R1.fastq.gz	RNA-Seq	4.7 GB	link
—	shTRNAU1AP_1_R1.fastq.gz	RNA-Seq	5.6 GB	link
—	shTRNAU1AP_1_R1.fastq.gz	RNA-Seq	5.6 GB	link
—	shTRNAU1AP_2_R1.fastq.gz	RNA-Seq	4.8 GB	link
—	shTRNAU1AP_2_R1.fastq.gz	RNA-Seq	4.8 GB	link
—	shTRNAU1AP_3_R1.fastq.gz	RNA-Seq	5.6 GB	link
—	shTRNAU1AP_3_R1.fastq.gz	RNA-Seq	5.6 GB	link