GSE73853
GSE GEOTranscriptome analysis of diverse cell types infected with human cytomegalovirus [RNA-Seq]
Organism:
Homo sapiens
Platform:
GPL11154
Samples:
13
Experiment Types:
Expression profiling by high throughput sequencing
Submitted:
Oct 08 2015
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/PRJNA299678
SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRP065236
Summary
Comprehensive RNA sequencing and splicing-sensitive microarray analysis of three diverse cell types infected with human cytomegalovirus (HCMV), including primary fibroblasts (HFFs), endothelial cells (ECs), and neural progenitors (NPCs) derived from embryonic stem cells. This global analysis includes both host and viral gene expression measurements, and an in-depth assessment of alternative RNA processing events. Extended comparisons were conducted through RNA sequencing analysis of human herpes simplex virus (HSV)-2 and human immunodeficiency virus type 1 (HIV-1) infections.
Overall Design
Deep sequencing analysis component of the study. RNA-seq measurements of host and virus gene expression, and RNA processing events.
Analysis (3 steps)
View Data Processing
Processing steps for GSE73853
- RNA-seq raw reads were trimmed for adaptor sequences or low-quality bases and mapped to both the human genome (hg19 build) and the HCMV Merlin genome (Genbank AY446894.2) with GSNAP, with additional filtering for repetitive regions.
- Virus-mapping reads were obtained from the HSV-2 and HIV-1 samples using Genbank accessions NC_001798.1 and K03455.1, respectively.
- Genome coverage files for visualization (bigWig format) were generated using UCSC tools bedGraphToBigWig and genomeCoverageBed, and strand-corrected.
Supplementary Files (1)
GSE73853_RAW.tar
Download
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 (13) and Runs (13)
Total: 125212 MBGSM1904488: HFF_Mock_48h; Homo sapiens; RNA-Seq
Sample: SRS1124443
BioProject: PRJNA299678
BioSample: SAMN04201209
Platform: ILLUMINA
Instrument: Illumina HiSeq 2000
Organism: Homo sapiens
Sample attributes
source_name: HFF_Mock_48h
cell type: HFF cells
infection: mock
time: 48h
Original files (1)
HFF_Mock_48h
Runs (1)
| Run | Spots | Bases | Size (MB) | Files | Link |
|---|---|---|---|---|---|
| SRR2747462 | 133221948 | 13455416748 | 7910.73 | HFF_Mock_48h.fastq.gz, SRR2747462, SRR2747462.sralite | SRA |
GSM1904489: HFF_InfectedHCMVTB40E_48h; Homo sapiens; RNA-Seq
Sample: SRS1124442
BioProject: PRJNA299678
BioSample: SAMN04201210
Platform: ILLUMINA
Instrument: Illumina HiSeq 2000
Organism: Homo sapiens
Sample attributes
source_name: HFF_InfectedHCMVTB40E_48h
cell type: HFF cells
infection: HCMV (strain TB40E)
time: 48h
Original files (1)
HFF_InfectedHCMVTB40E_48h
Runs (1)
| Run | Spots | Bases | Size (MB) | Files | Link |
|---|---|---|---|---|---|
| SRR2747463 | 193155843 | 19508740143 | 12001.72 | HFF_InfectedHCMVTB40E_48h.fastq.gz, SRR2747463, SRR2747463.sralite | SRA |
GSM1904490: HFF_InfectedHCMVTB40E_96h; Homo sapiens; RNA-Seq
Sample: SRS1124441
BioProject: PRJNA299678
BioSample: SAMN04201211
Platform: ILLUMINA
Instrument: Illumina HiSeq 2000
Organism: Homo sapiens
Sample attributes
source_name: HFF_InfectedHCMVTB40E_96h
cell type: HFF cells
infection: HCMV (strain TB40E)
time: 96h
Original files (1)
HFF_InfectedHCMVTB40E_96h
Runs (1)
| Run | Spots | Bases | Size (MB) | Files | Link |
|---|---|---|---|---|---|
| SRR2747464 | 183380340 | 18521414340 | 11256.86 | HFF_InfectedHCMVTB40E_96h.fastq.gz, SRR2747464, SRR2747464.sralite | SRA |
GSM1904491: EC_Mock_48h; Homo sapiens; RNA-Seq
Sample: SRS1124440
BioProject: PRJNA299678
BioSample: SAMN04201212
Platform: ILLUMINA
Instrument: Illumina HiSeq 2000
Organism: Homo sapiens
Sample attributes
source_name: EC_Mock_48h
cell type: EC cells
infection: mock
time: 48h
Original files (1)
EC_Mock_48h
Runs (1)
| Run | Spots | Bases | Size (MB) | Files | Link |
|---|---|---|---|---|---|
| SRR2747465 | 174000823 | 17574083123 | 10382.75 | EC_Mock_48h.fastq.gz, SRR2747465, SRR2747465.sralite | SRA |
GSM1904492: EC_InfectedHCMVTB40E_48h; Homo sapiens; RNA-Seq
Sample: SRS1124439
BioProject: PRJNA299678
BioSample: SAMN04201213
Platform: ILLUMINA
Instrument: Illumina HiSeq 2000
Organism: Homo sapiens
Sample attributes
source_name: EC_InfectedHCMVTB40E_48h
cell type: EC cells
infection: HCMV (strain TB40E)
time: 48h
Original files (1)
EC_InfectedHCMVTB40E_48h
Runs (1)
| Run | Spots | Bases | Size (MB) | Files | Link |
|---|---|---|---|---|---|
| SRR2747466 | 174883617 | 17663245317 | 10739.41 | EC_InfectedHCMVTB40E_48h.fastq.gz, SRR2747466, SRR2747466.sralite | SRA |
GSM1904493: EC_InfectedHCMVTB40E_96h; Homo sapiens; RNA-Seq
Sample: SRS1124437
BioProject: PRJNA299678
BioSample: SAMN04201214
Platform: ILLUMINA
Instrument: Illumina HiSeq 2000
Organism: Homo sapiens
Sample attributes
source_name: EC_InfectedHCMVTB40E_96h
cell type: EC cells
infection: HCMV (strain TB40E)
time: 96h
Original files (1)
EC_InfectedHCMVTB40E_96h
Runs (1)
| Run | Spots | Bases | Size (MB) | Files | Link |
|---|---|---|---|---|---|
| SRR2747467 | 205585245 | 20764109745 | 13056.08 | EC_InfectedHCMVTB40E_96h.fastq.gz, SRR2747467, SRR2747467.sralite | SRA |
GSM1904494: NPC_Mock_48h; Homo sapiens; RNA-Seq
Sample: SRS1124438
BioProject: PRJNA299678
BioSample: SAMN04201215
Platform: ILLUMINA
Instrument: Illumina HiSeq 2000
Organism: Homo sapiens
Sample attributes
source_name: NPC_Mock_48h
cell type: NPC cells (ES-derived)
infection: mock
time: 48h
Original files (1)
NPC_Mock_48h
Runs (1)
| Run | Spots | Bases | Size (MB) | Files | Link |
|---|---|---|---|---|---|
| SRR2747468 | 221423918 | 22363815718 | 13858.61 | NPC_Mock_48h.fastq.gz, SRR2747468, SRR2747468.sralite | SRA |
GSM1904495: NPC_InfectedHCMVTB40E_48h; Homo sapiens; RNA-Seq
Sample: SRS1124436
BioProject: PRJNA299678
BioSample: SAMN04201216
Platform: ILLUMINA
Instrument: Illumina HiSeq 2000
Organism: Homo sapiens
Sample attributes
source_name: NPC_InfectedHCMVTB40E_48h
cell type: NPC cells (ES-derived)
infection: HCMV (strain TB40E)
time: 48h
Original files (1)
NPC_InfectedHCMVTB40E_48h
Runs (1)
| Run | Spots | Bases | Size (MB) | Files | Link |
|---|---|---|---|---|---|
| SRR2747469 | 231102951 | 23341398051 | 13965.77 | NPC_InfectedHCMVTB40E_48h.fastq.gz, SRR2747469, SRR2747469.sralite | SRA |
GSM1904496: NPC_InfectedHCMVTB40E_96h; Homo sapiens; RNA-Seq
Sample: SRS1124435
BioProject: PRJNA299678
BioSample: SAMN04201217
Platform: ILLUMINA
Instrument: Illumina HiSeq 2000
Organism: Homo sapiens
Sample attributes
source_name: NPC_InfectedHCMVTB40E_96h
cell type: NPC cells (ES-derived)
infection: HCMV (strain TB40E)
time: 96h
Original files (1)
NPC_InfectedHCMVTB40E_96h
Runs (1)
| Run | Spots | Bases | Size (MB) | Files | Link |
|---|---|---|---|---|---|
| SRR2747470 | 216498620 | 21866360620 | 12740.01 | NPC_InfectedHCMVTB40E_96h.fastq.gz, SRR2747470, SRR2747470.sralite | SRA |
GSM1904497: HFF_MockforHSV_8h; Homo sapiens; RNA-Seq
Sample: SRS1124434
BioProject: PRJNA299678
BioSample: SAMN04201218
Platform: ILLUMINA
Instrument: Illumina HiSeq 2000
Organism: Homo sapiens
Sample attributes
source_name: HFF_MockforHSV_8h
cell type: HFF cells
infection: mock
time: 8h
Original files (1)
HFF_MockforHSV_8h
Runs (1)
| Run | Spots | Bases | Size (MB) | Files | Link |
|---|---|---|---|---|---|
| SRR2747471 | 49979804 | 2498990200 | 1607.9 | HFF_MockforHSV_8h.fastq.gz, SRR2747471, SRR2747471.sralite | SRA |
GSM1904498: HFF_InfectedHSV2_8h; Homo sapiens; RNA-Seq
Sample: SRS1124433
BioProject: PRJNA299678
BioSample: SAMN04201219
Platform: ILLUMINA
Instrument: Illumina HiSeq 2000
Organism: Homo sapiens
Sample attributes
source_name: HFF_InfectedHSV2_8h
cell type: HFF cells
infection: HSV2
time: 8h
Original files (1)
HFF_InfectedHSV2_8h
Runs (1)
| Run | Spots | Bases | Size (MB) | Files | Link |
|---|---|---|---|---|---|
| SRR2747472 | 40464251 | 2023212550 | 1368.5 | HFF_InfectedHSV2_8h.fastq.gz, SRR2747472, SRR2747472.sralite | SRA |
GSM2306702: Tcell_Control_5d; Homo sapiens; RNA-Seq
Sample: SRS1683471
BioProject: PRJNA299678
BioSample: SAMN05755901
Platform: ILLUMINA
Instrument: Illumina HiSeq 2000
Organism: Homo sapiens
Sample attributes
source_name: Tcell_Control_5d
cell type: T cells
infection: control
time: 5d
Original files (1)
Tcell_Control_5d
Runs (1)
| Run | Spots | Bases | Size (MB) | Files | Link |
|---|---|---|---|---|---|
| SRR4209731 | 127439591 | 12743959100 | 7331.18 | Tcell_Control_5d.fastq.gz, SRR4209731, SRR4209731.sralite | SRA |
GSM2306703: Tcell_InfectedHIV1_5d; Homo sapiens; RNA-Seq
Sample: SRS1683472
BioProject: PRJNA299678
BioSample: SAMN05755900
Platform: ILLUMINA
Instrument: Illumina HiSeq 2000
Organism: Homo sapiens
Sample attributes
source_name: Tcell_InfectedHIV1_5d
cell type: T cells
infection: HIV1
time: 5d
Original files (1)
Tcell_InfectedHIV1_5d
Runs (1)
| Run | Spots | Bases | Size (MB) | Files | Link |
|---|---|---|---|---|---|
| SRR4209732 | 150512324 | 15051232400 | 8992.11 | Tcell_InfectedHIV1_5d.fastq.gz, SRR4209732, SRR4209732.sralite | SRA |
Linked Publications (1)
RNA-binding protein CPEB1 remodels host and viral RNA landscapes.
Nature structural & molecular biology · 2016
Data Files (13)
| Accession | File Name | Stored Type | Output Type | Mapping Assembly | Size | Download | |
|---|---|---|---|---|---|---|---|
| — | EC_InfectedHCMVTB40E_48h.fastq.gz | RNA-Seq | 10.5 GB | link | |||
| — | EC_InfectedHCMVTB40E_96h.fastq.gz | RNA-Seq | 12.8 GB | link | |||
| — | EC_Mock_48h.fastq.gz | RNA-Seq | 10.1 GB | link | |||
| — | HFF_InfectedHCMVTB40E_48h.fastq.gz | RNA-Seq | 11.7 GB | link | |||
| — | HFF_InfectedHCMVTB40E_96h.fastq.gz | RNA-Seq | 11.0 GB | link | |||
| — | HFF_InfectedHSV2_8h.fastq.gz | RNA-Seq | 1.3 GB | link | |||
| — | HFF_Mock_48h.fastq.gz | RNA-Seq | 7.7 GB | link | |||
| — | HFF_MockforHSV_8h.fastq.gz | RNA-Seq | 1.6 GB | link | |||
| — | NPC_InfectedHCMVTB40E_48h.fastq.gz | RNA-Seq | 13.6 GB | link | |||
| — | NPC_InfectedHCMVTB40E_96h.fastq.gz | RNA-Seq | 12.4 GB | link | |||
| — | NPC_Mock_48h.fastq.gz | RNA-Seq | 13.5 GB | link | |||
| — | Tcell_Control_5d.fastq.gz | RNA-Seq | 7.2 GB | link | |||
| — | Tcell_InfectedHIV1_5d.fastq.gz | RNA-Seq | 8.8 GB | link |