GSE86791

GSE GEO

View on GEO Export SRA CSV

RNA binding protein CPEB1 remodels host and viral RNA landscapes [RNA-Seq]

Organism: Homo sapiens

Platform: GPL15520

Samples: 9

Experiment Types:

Expression profiling by high throughput sequencing Other

Submitted: Sep 09 2016

Last Updated: May 15 2019

Status: Public on Sep 17 2016

Contact: Gene,,Yeo (UCSD)

Relations

SubSeries of: GSE74250 BioProject: https://www.ncbi.nlm.nih.gov/bioproject/PRJNA342503 SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRP087936

Summary

In this study, we report that HCMV infection results in widespread alternative splicing (AS), shorter 3â²-untranslated regions (3â²UTRs) and polyA tail lengthening in host genes and CPEB1 depletion reverses infection-related post-transcriptional changes.

Overall Design

We performed RNA-seq for Mock (Non-targeting siRNA), human Cytomegalovirus (HCMV) with non-targeting siRNA, and CPEB1 siRNA treated human foreskin fibroblasts (HFFs). We also performed RNA-seq for lentivirus mediated GFP overexpression (OE) and CPEB1 overexpression human foreskin fibroblasts. Lastly, we performed TAIL-seq for Mock (Non-targeting siRNA), human Cytomegalovirus (HCMV) with non-targeting siRNA, and CPEB1 siRNA treated HFFs.

Analysis (16 steps)

View Data Processing

Processing steps for GSE86791

RNA-seq data was aligned to the human hg19 genome build using Olego and Star aligners, and alternative splicing and alternative polyadenylation were estimated as described below.
Quantas software as described in Charizanis et al, 2012, Neuron, was used to estimate alternative splicing.
Olego aligned alignment files were used to count observed junction reads for each exon.
Weighted number of exon or exon-junction fragments uniquely supporting the inclusion or skipping isoform of each cassette exon and a probability score was assigned to each isoform.
A Fisherâs exact test was used to evaluate the statistical significance of splicing changes using both exon and exon-junction fragments, followed by Benjamini multiple testing correction to estimate the false discovery rate (FDR).
In addition, inclusion or exclusion junction reads were used to calculate the proportional change of exon inclusion (dI).
See documentation at http://zhanglab.c2b2.columbia.edu/index.php/Quantas_Documentation.
Tandem UTR isoform analysis was performed with the MISO algorithm v0.5.2 using default settings as described in Katz et al, Nature, 2010, except for use of custom 3â²UTR isoform annotations.

Showing first 8 steps.

Supplementary Files (4)

GSE86791_RAW.tar Download

GSE86791_Table_S3_Host_APA_events.xlsx Download

GSE86791_Table_S6_AS_Changes_siCPEB1_CPEB1OE_HFFs_RNA-seq.xlsx Download

GSE86791_Table_S8_PolyA_Tail_Lengths_TAIL-seq.xlsx Download

GEO Samples (9)

GSM2308766 GSM2308767 GSM2308768 GSM2308769 GSM2308770 GSM2308771 GSM2308772 GSM2308773 GSM2308774

Dataset Citations (1)

RNA-binding protein CPEB1 remodels host and viral RNA landscapes.

PMID 27775709 · 2016 · Nature structural & molecular biology

Ranjan Batra, Thomas J Stark, Alex E. Clark, Jean-Philippe Belzile, Emily C Wheeler, Brian A Yee, Hui Huang, Chelsea Gelboin-Burkhart, Stephanie C Huelga, Stefan Aigner, Brett T Roberts, Tomas J Bos, Shashank Sathe, John Paul Donohue, Frank Rigo, Manuel Ares, Deborah H Spector, Gene W Yeo

SRA Experiments (9) and Runs (9)

Total: 28644 MB

SRX2155846 SRP087936 RNA-Seq PAIRED

GSM2308766: Mock infected Non-targeting siRNA treated human foreskin fibroblasts [RNA-Seq]; Homo sapiens; RNA-Seq

Sample: SRS1685851

BioProject: PRJNA342503

BioSample: SAMN05761519

Platform: ILLUMINA

Instrument: Illumina HiSeq 4000

Organism: Homo sapiens

Sample attributes

source_name: Mock infected Non-targeting siRNA treated human foreskin fibroblasts

cell type: HFF cells

infection: Mock Infected (serum with no HCMV)

treatment: Non-Targeting siRNA treatment

Original files (1)

Mock infected Non-targeting siRNA treated human foreskin fibroblasts

Runs (1)

Run	Spots	Bases	Size (MB)	Files	Link
SRR4228549	54728920	10945784000	4949.29	Mock_R1_001.fastq.gz, Mock_R2_001.fastq.gz, SRR4228549, SRR4228549.sr…	SRA

SRX2155847 SRP087936 RNA-Seq PAIRED

GSM2308767: HCMV infected Non-targeting siRNA treated human foreskin fibroblasts [RNA-Seq]; Homo sapiens; RNA-Seq

Sample: SRS1685852

BioProject: PRJNA342503

BioSample: SAMN05761518

Platform: ILLUMINA

Instrument: Illumina HiSeq 4000

Organism: Homo sapiens

Sample attributes

source_name: HCMV infected Non-targeting siRNA treated human foreskin fibroblasts

cell type: HFF cells

infection: HCMV infected

treatment: Non-Targeting siRNA treatment

Original files (1)

HCMV infected Non-targeting siRNA treated human foreskin fibroblasts

Runs (1)

Run	Spots	Bases	Size (MB)	Files	Link
SRR4228550	82374756	16474951200	5986.61	HCMV_R1_001.fastq.gz, HCMV_R2_001.fastq.gz, SRR4228550, SRR4228550.sr…	SRA

SRX2155848 SRP087936 RNA-Seq PAIRED

GSM2308768: HCMV infected siCPEB1 siRNA treated human foreskin fibroblasts [RNA-Seq]; Homo sapiens; RNA-Seq

Sample: SRS1685853

BioProject: PRJNA342503

BioSample: SAMN05761517

Platform: ILLUMINA

Instrument: Illumina HiSeq 4000

Organism: Homo sapiens

Sample attributes

source_name: HCMV infected siCPEB1 siRNA treated human foreskin fibroblasts

cell type: HFF cells

infection: HCMV infected

treatment: CPEB1 siRNA treatment

Original files (1)

HCMV infected siCPEB1 siRNA treated human foreskin fibroblasts

Runs (1)

Run	Spots	Bases	Size (MB)	Files	Link
SRR4228551	48484914	9696982800	4317.8	siCPEB1_R1_001.fastq.gz, siCPEB1_R2_001.fastq.gz, SRR4228551, SRR4228…	SRA

SRX2155849 SRP087936 RNA-Seq PAIRED

GSM2308769: Lentivirus mediated GFP overexpression in human foreskin fibroblasts [RNA-Seq]; Homo sapiens; RNA-Seq

Sample: SRS1685854

BioProject: PRJNA342503

BioSample: SAMN05761521

Platform: ILLUMINA

Instrument: Illumina HiSeq 4000

Organism: Homo sapiens

Sample attributes

source_name: Lentivirus mediated GFP overexpression in human foreskin fibroblasts

cell type: HFF cells

genotype/variation: Lentivirus mediated GFP overexpression

treatment: Puromycin selection - 5 days

Original files (1)

Lentivirus mediated GFP overexpression in human foreskin fibroblasts

Runs (1)

Run	Spots	Bases	Size (MB)	Files	Link
SRR4228552	63785289	12757057800	5755.09	GFP_OE_R1_001.fastq.gz, GFP_OE_R2_001.fastq.gz, SRR4228552, SRR422855…	SRA

SRX2155850 SRP087936 RNA-Seq PAIRED

GSM2308770: Lentivirus mediated CPEB1 overexpression in human foreskin fibroblasts-1 [RNA-Seq]; Homo sapiens; RNA-Seq

Sample: SRS1685855

BioProject: PRJNA342503

BioSample: SAMN05761520

Platform: ILLUMINA

Instrument: Illumina HiSeq 4000

Organism: Homo sapiens

Sample attributes

source_name: Lentivirus mediated CPEB1 overexpression in human foreskin fibroblasts

cell type: HFF cells

genotype/variation: Lentivirus mediated CPEB1 overexpression

treatment: Puromycin selection - 5 days

Original files (1)

Lentivirus mediated CPEB1 overexpression in human foreskin fibroblasts

Runs (1)

Run	Spots	Bases	Size (MB)	Files	Link
SRR4228553	56989214	11397842800	5131.87	CPEB1_OE1_R1_001.fastq.gz, CPEB1_OE1_R2_001.fastq.gz, SRR4228553, SRR…	SRA

SRX2155851 SRP087936 RNA-Seq PAIRED

GSM2308771: Lentivirus mediated CPEB1 overexpression in human foreskin fibroblasts-2 [RNA-Seq]; Homo sapiens; RNA-Seq

Sample: SRS1685856

BioProject: PRJNA342503

BioSample: SAMN05761516

Platform: ILLUMINA

Instrument: Illumina HiSeq 4000

Organism: Homo sapiens

Sample attributes

source_name: Lentivirus mediated CPEB1 overexpression in human foreskin fibroblasts

cell type: HFF cells

genotype/variation: Lentivirus mediated CPEB1 overexpression

treatment: Puromycin selection - 5 days

Original files (1)

Lentivirus mediated CPEB1 overexpression in human foreskin fibroblasts

Runs (1)

Run	Spots	Bases	Size (MB)	Files	Link
SRR4228554	24290544	4858108800	2181.66	CPEB1_OE2_R1_001.fastq.gz, CPEB1_OE2_R2_001.fastq.gz, SRR4228554, SRR…	SRA

SRX2155852 SRP087936 OTHER PAIRED

GSM2308772: Mock infected Non-targeting siRNA treated human foreskin fibroblasts [Tail-Seq]; Homo sapiens; OTHER

Sample: SRS1685857

BioProject: PRJNA342503

BioSample: SAMN05761515

Platform: ILLUMINA

Instrument: Illumina MiSeq

Organism: Homo sapiens

Sample attributes

source_name: Mock infected Non-targeting siRNA treated human foreskin fibroblasts

cell type: HFF cells

infection: Mock Infected (serum with no HCMV)

treatment: Non-Targeting siRNA treatment

Original files (1)

Mock infected Non-targeting siRNA treated human foreskin fibroblasts

Runs (1)

Run	Spots	Bases	Size (MB)	Files	Link
SRR4228555	2724320	138940320	102.62	uninf_R3.fastq.gz, uninf_R5.fastq.gz, SRR4228555, SRR4228555.sralite	SRA

SRX2155853 SRP087936 OTHER PAIRED

GSM2308773: HCMV infected Non-targeting siRNA treated human foreskin fibroblasts [Tail-Seq]; Homo sapiens; OTHER

Sample: SRS1685858

BioProject: PRJNA342503

BioSample: SAMN05761514

Platform: ILLUMINA

Instrument: Illumina MiSeq

Organism: Homo sapiens

Sample attributes

source_name: HCMV infected Non-targeting siRNA treated human foreskin fibroblasts

cell type: HFF cells

infection: HCMV infected

treatment: Non-Targeting siRNA treatment

Original files (1)

HCMV infected Non-targeting siRNA treated human foreskin fibroblasts

Runs (1)

Run	Spots	Bases	Size (MB)	Files	Link
SRR4228556	2589383	132058533	96.53	inf_R3.fastq.gz, inf_R5.fastq.gz, SRR4228556, SRR4228556.sralite	SRA

SRX2155854 SRP087936 OTHER PAIRED

GSM2308774: HCMV infected siCPEB1 siRNA treated human foreskin fibroblasts [Tail-Seq]; Homo sapiens; OTHER

Sample: SRS1685859

BioProject: PRJNA342503

BioSample: SAMN05761513

Platform: ILLUMINA

Instrument: Illumina MiSeq

Organism: Homo sapiens

Sample attributes

source_name: HCMV infected siCPEB1 siRNA treated human foreskin fibroblasts

cell type: HFF cells

infection: HCMV infected

treatment: CPEB1 siRNA treatment

Original files (1)

HCMV infected siCPEB1 siRNA treated human foreskin fibroblasts

Runs (1)

Run	Spots	Bases	Size (MB)	Files	Link
SRR4228557	3258746	166196046	122.21	infCPEB1_R3.fastq.gz, infCPEB1_R5.fastq.gz, SRR4228557, SRR4228557.sr…	SRA

Linked Publications (1)

RNA-binding protein CPEB1 remodels host and viral RNA landscapes.

Nature structural & molecular biology · 2016

Data Files (9)

Accession	File Name	Stored Type	Size	Download
—	infCPEB1_R3.fastq.gz	OTHER	122.2 MB	link
—	inf_R3.fastq.gz	OTHER	96.5 MB	link
—	uninf_R3.fastq.gz	OTHER	102.6 MB	link
—	CPEB1_OE1_R1_001.fastq.gz	RNA-Seq	5.0 GB	link
—	CPEB1_OE2_R1_001.fastq.gz	RNA-Seq	2.1 GB	link
—	GFP_OE_R1_001.fastq.gz	RNA-Seq	5.6 GB	link
—	HCMV_R1_001.fastq.gz	RNA-Seq	5.8 GB	link
—	Mock_R1_001.fastq.gz	RNA-Seq	4.8 GB	link
—	siCPEB1_R1_001.fastq.gz	RNA-Seq	4.2 GB	link