GSE113193

GSE GEO

View on GEO Export SRA CSV

Tissue-selective restriction of RNA editing of CaV1.3 by splicing factor SRSF9

Organism: Homo sapiens

Platform: GPL18573

Samples: 5

Experiment Types:

Other

Submitted: Apr 16 2018

Last Updated: Mar 26 2019

Status: Public on Apr 17 2018

Contact: Gene,W,Yeo (University of California, San Diego)

Relations

BioProject: https://www.ncbi.nlm.nih.gov/bioproject/PRJNA450408 SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRP140530

Summary

Adenosine DeAminases acting on RNA (ADAR) catalyzes adenosine-to-inosine (A-to-I) conversion within RNA duplex structures. While A-to-I editing is often dynamically regulated in a spatial-temporal manner, the mechanisms underlying its tissue-selective restriction remain elusive. We have previously reported that transcripts of voltage-gated calcium channel CaV1.3 are subject to brain-selective A-to-I RNA editing by ADAR2. Here, we show that editing of CaV1.3 mRNA is dependent on a 40 bp RNA duplex formed between exon 41 and an evolutionarily conserved editing site complementary sequence (ECS) located within the preceding intron. Heterologous expression of a mouse minigene that contained the ECS, intermediate intronic sequence and exon 41 with ADAR2 yielded robust editing. Interestingly, editing of CaV1.3 was potently inhibited by serine/arginine-rich splicing factor 9 (SRSF9). Mechanistically, the inhibitory effect of SRSF9 required direct RNA interaction. Selective down-regulation of SRSF9 in neurons provides a basis for the neuron-specific editing of CaV1.3 transcripts.

Overall Design

eCLIP-seq for HA-SRSF9 in HEK293 cells

Analysis (32 steps)

View Data Processing

Processing steps for GSE113193

Takes output from raw files.
Run to trim off both 5â and 3â adapters on both reads.
Command: quality-cutoff 6 -m 18 -a NNNNNAGATCGGAAGAGCACACGTCTGAACTCCAGTCAC -g CTTCCGATCTACAAGTT -g CTTCCGATCTTGGTCCT -A AACTTGTAGATCGGA -A AGGACCAAGATCGGA -A ACTTGTAGATCGGAA -A GGACCAAGATCGGAA -A CTTGT AGATCGGAAG -A GACCAAGATCGGAAG -A TTGTAGATCGGAAGA -A ACCAAGATCGGAAGA -A TGTAGATCGGAAGAG -A CCAAGATCGGAAGAG -A GTAGATCGGAAGAGC -A CAAGATCGGAAGAGC -A TAGATCGGAAGAGCG -A AAGATCGGAAGAGCG -A AGATCGGAAGAGCGT -A GATCGGAAGAGCGTC -A ATCGGAAGAGCGTCG -A TCGGAAGAGCGTCGT -A CGGAAGAGCGTCGTG -A GGAAGAGCGTCGTGT -o /full/path/to/files/file_R1.C01.fastq.gz.adapterTrim.fastq.gz -p /full/path/to/files/file_R2.C01.fastq.gz.adapterTrim.fastq.gz /full/path/to/files/file_R1.C01.fastq.gz /full/path/to/files/file_R2.C01.fastq.gz > /full/path/to/files/file_R1.C01.fastq.gz.adapterTrim.metrics
Takes output from cutadapt round 1.
Run to trim off the 3â adapters on read 2, to control for double ligation events.
Command: cutadapt -f fastq --match-read-wildcards --times 1 -e 0.1 -O 5 --quality-cutoff 6 -m 18 -A AACTTGTAGATCGGA -A AGGACCAAGATCGGA -A ACTTGTAGATCGGAA -A GGACCAAGATCGGAA -A CTTGTAGATCGGAAG -A GACCAAGATCGGAAG -A TTGTAGATCGGAAGA -A ACCAAGATCGGAAGA -A TGTAGATCGGAAGAG -A CCAAGATCGGAAGAG -A GTAGATCGGAAGAGC -A CAAGATCGGAAGAGC -A TAGATCGGAAGAGCG -A AAGATCGGAAGAGCG -A AGATCGGAAGAGCGT -A GATCGGAAGAGCGTC -A ATCGGAAGAGCGTCG -A TCGGAAGAGCGTCGT -A CGGAAGAGCGTCGTG -A GGAAGAGCGTCGTGT -o /full/path/to/files/file_R1.C01.fastq.gz.adapterTrim.round2.fastq.gz -p /full/path/to/files/file_R2.C01.fastq.gz.adapterTrim.round2.fastq.gz /full/path/to/files/file_R1.C01.fastq.gz.adapterTrim.fastq.gz /full/path/to/files/file_R2.C01.fastq.gz.adapterTrim.fastq.gz > /full/path/to/files/file_R1.C01.fastq.gz.adapterTrim.round2.metrics
Takes output from cutadapt round 2.
Maps to human specific version of RepBase used to remove repetitive elements, helps control for spurious artifacts from rRNA (& other) repetitive reads.

Showing first 8 steps.

Supplementary Files (1)

GSE113193_RAW.tar Download

GEO Samples (5)

GSM3099820 GSM3099821 GSM3099822 GSM3099823 GSM3099824

Dataset Citations (1)

Tissue-selective restriction of RNA editing of CaV1.3 by splicing factor SRSF9.

PMID 29733375 · 2018 · Nucleic acids research

Hua Huang, Katannya Kapeli, Wenhao Jin, Yuk Peng Wong, Thiruma Valavan Arumugam, Joanne Huifen Koh, Sumitra Srimasorn, Karthik Mallilankaraman, John Jia En Chua, Gene W Yeo, Tuck Wah Soong

SRA Experiments (5) and Runs (5)

Total: 4906 MB

SRX3942977 SRP140530 OTHER PAIRED

GSM3099820: Input replicate 1; Homo sapiens; OTHER

Sample: SRS3173537

BioProject: PRJNA450408

BioSample: SAMN08937966

Platform: ILLUMINA

Instrument: NextSeq 500

Organism: Homo sapiens

Sample attributes

source_name: HEK293T

sample type: input

Original files (1)

HEK293T

Runs (1)

Run	Spots	Bases	Size (MB)	Files	Link
SRR7010498	36794952	3712981935	1381.67	SRSF9-rep1-input_S4_R1_001.fastq.gz, SRSF9-rep1-input_S4_R2_001.fastq…	SRA

SRX3942978 SRP140530 OTHER PAIRED

GSM3099821: Input replicate 2; Homo sapiens; OTHER

Sample: SRS3173538

BioProject: PRJNA450408

BioSample: SAMN08937965

Platform: ILLUMINA

Instrument: NextSeq 500

Organism: Homo sapiens

Sample attributes

source_name: HEK293T

sample type: input

Original files (1)

HEK293T

Runs (1)

Run	Spots	Bases	Size (MB)	Files	Link
SRR7010499	36117757	3629044617	1366.54	SRSF9-rep2-input_S1_R1_001.fastq.gz, SRSF9-rep2-input_S1_R2_001.fastq…	SRA

SRX3942979 SRP140530 OTHER PAIRED

GSM3099822: IgG; Homo sapiens; OTHER

Sample: SRS3173539

BioProject: PRJNA450408

BioSample: SAMN08937964

Platform: ILLUMINA

Instrument: NextSeq 500

Organism: Homo sapiens

Sample attributes

source_name: HEK293T

sample type: IgG

antibody company: Sino Biotchnology

Original files (1)

HEK293T

Runs (1)

Run	Spots	Bases	Size (MB)	Files	Link
SRR7010500	13097421	1303287650	488.63	IgG-IP_S3_R1_001.fastq.gz, IgG-IP_S3_R2_001.fastq.gz, SRR7010500, SRR…	SRA

SRX3942980 SRP140530 OTHER PAIRED

GSM3099823: SRSF9 eCLIP replicate 1; Homo sapiens; OTHER

Sample: SRS3173540

BioProject: PRJNA450408

BioSample: SAMN08937963

Platform: ILLUMINA

Instrument: NextSeq 500

Organism: Homo sapiens

Sample attributes

source_name: HEK293T

tag: HA

sample type: SRSF9

antibody company: Sigma

Original files (1)

HEK293T

Runs (1)

Run	Spots	Bases	Size (MB)	Files	Link
SRR7010501	25325225	2555868332	972.04	SRSF9-rep1-IP_S2_R1_001.fastq.gz, SRSF9-rep1-IP_S2_R2_001.fastq.gz, S…	SRA

SRX3942981 SRP140530 OTHER PAIRED

GSM3099824: SRSF9 eCLIP replicate 2; Homo sapiens; OTHER

Sample: SRS3173541

BioProject: PRJNA450408

BioSample: SAMN08937962

Platform: ILLUMINA

Instrument: NextSeq 500

Organism: Homo sapiens

Sample attributes

source_name: HEK293T

tag: HA

sample type: SRSF9

antibody company: Sigma

Original files (1)

HEK293T

Runs (1)

Run	Spots	Bases	Size (MB)	Files	Link
SRR7010502	18742629	1890087062	696.71	SRSF9-rep2-IP_S5_R1_001.fastq.gz, SRSF9-rep2-IP_S5_R2_001.fastq.gz, S…	SRA

Linked Publications (1)

Tissue-selective restriction of RNA editing of CaV1.3 by splicing factor SRSF9.

Nucleic acids research · 2018

Data Files (5)

Accession	File Name	Stored Type	Size	Download
—	IgG-IP_S3_R1_001.fastq.gz	OTHER	488.6 MB	link
—	SRSF9-rep1-input_S4_R1_001.fastq.gz	OTHER	1.3 GB	link
—	SRSF9-rep1-IP_S2_R1_001.fastq.gz	OTHER	972.0 MB	link
—	SRSF9-rep2-input_S1_R1_001.fastq.gz	OTHER	1.3 GB	link
—	SRSF9-rep2-IP_S5_R1_001.fastq.gz	OTHER	696.7 MB	link