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GSE80664

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Transcriptome-wide mRNA alterations in Streptozotocin induced Type I diabetic mouse heart

Organism: Mus musculus
Platform: GPL15103
Samples: 5
Experiment Types:
Expression profiling by high throughput sequencing
Submitted: Apr 26 2016
Last Updated: May 15 2019
Status: Public on May 26 2016
Contact: Muge,N,Kuyumcu-Martinez (University of Texas Medical Branch)

Relations

BioProject: https://www.ncbi.nlm.nih.gov/bioproject/PRJNA321413 SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRP074888

Summary

We sequenced mRNA from Left Ventricles of Streptozotocin induced Type I diabetic mouse hearts or mock treated controls at 4 weeks post-treatment in order to assess alternative splicing changes.

Overall Design

Heart mRNA profiles of Control and Diabetic (STZ:T1D) mice were generated by deep sequencing using Illumina HiSeq 1000.

Analysis (9 steps)

View Data Processing
Processing steps for GSE80664
  1. Base calling was performed with CASAVA 1.8.2
  2. Sequences were trimmed then aligned to the mm9 mouse genome using TOPHAT
  3. Probabilities of isoform abundances were computed using MISO
  4. Data was filtered based on a Bayes factor of at least 1
  5. Additional details are included in Verma, S.K., Deshmukh, V., Liu, P., Nutter, C.A., Espejo, R., Hung, M.L., Wang, G.S., Yeo, G.W., and Kuyumcu-Martinez, M.N. (2013).
  6. Reactivation of fetal splicing programs in diabetic hearts is mediated by protein kinase C signaling.
  7. The Journal of biological chemistry 288, 35372-35386.
  8. processed data files format and content: Proccessed data is MISO analysis of skipped exons in comparisions between control and diabetic samples.
Showing first 8 steps.

Supplementary Files (6)

GSE80664_MISO.SE_S5407vS11.txt.gz Download
GSE80664_MISO.SE_S5407vS15.txt.gz Download
GSE80664_MISO.SE_S5407vS24.txt.gz Download
GSE80664_MISO.SE_S5408vS11.txt.gz Download
GSE80664_MISO.SE_S5408vS15.txt.gz Download
GSE80664_MISO.SE_S5408vS24.txt.gz Download
GEO Samples (5)
GSM2132563 GSM2132564 GSM2132565 GSM2132566 GSM2132567

Dataset Citations (1)

Dysregulation of RBFOX2 Is an Early Event in Cardiac Pathogenesis of Diabetes.
PMID 27239029 · 2016 · Cell reports
Curtis A Nutter, Elizabeth A Jaworski, Sunil K Verma, Vaibhav Deshmukh, Qiongling Wang, Olga B Botvinnik, Mario J Lozano, Ismail J Abass, Talha Ijaz, Allan R Brasier, Nisha J Garg, Xander H T Wehrens, Gene W Yeo, Muge N Kuyumcu-Martinez

SRA Experiments (5) and Runs (5)

Total: 64271 MB
SRX1757979 SRP074888 RNA-Seq PAIRED
GSM2132563: Control 1; Mus musculus; RNA-Seq
Sample: SRS1434275
BioProject: PRJNA321413
BioSample: SAMN04993342
Platform: ILLUMINA
Instrument: Illumina HiSeq 2000
Organism: Mus musculus
Sample attributes
source_name: Heart
strain: C57BL/6
tissue: Left Ventricle Heart
age: 12 weeks
treatment: Mock treatment: IP injection of citrate buffer
Original files (1)
Heart
Runs (1)
Run Spots Bases Size (MB) Files Link
SRR3499912 211356390 21135639000 12631.81 5407_NoIndex_L007_R1_001.fastq.gz, 5407_NoIndex_L007_R2_001.fastq.gz,… SRA
SRX1757980 SRP074888 RNA-Seq PAIRED
GSM2132564: Control 2; Mus musculus; RNA-Seq
Sample: SRS1434276
BioProject: PRJNA321413
BioSample: SAMN04993344
Platform: ILLUMINA
Instrument: Illumina HiSeq 2000
Organism: Mus musculus
Sample attributes
source_name: Heart
strain: C57BL/6
tissue: Left Ventricle Heart
age: 12 weeks
treatment: Mock treatment: IP injection of citrate buffer
Original files (1)
Heart
Runs (1)
Run Spots Bases Size (MB) Files Link
SRR3499913 259915408 25991540800 16807.68 5408_NoIndex_L008_R1_001.fastq.gz, 5408_NoIndex_L008_R2_001.fastq.gz,… SRA
SRX1757981 SRP074888 RNA-Seq PAIRED
GSM2132565: STZ:T1D 1; Mus musculus; RNA-Seq
Sample: SRS1434277
BioProject: PRJNA321413
BioSample: SAMN04993346
Platform: ILLUMINA
Instrument: Illumina HiSeq 2000
Organism: Mus musculus
Sample attributes
source_name: Heart
strain: C57BL/6
tissue: Left Ventricle Heart
age: 12 weeks
treatment: STZ treatment: IP injection of 70mg/kg streptezotocin 1/per day for 5 days.
Original files (1)
Heart
Runs (1)
Run Spots Bases Size (MB) Files Link
SRR3499914 192456292 19245629200 11167.13 11_NoIndex_L001_R1_001.fastq.gz, 11_NoIndex_L001_R2_001.fastq.gz, SRR… SRA
SRX1757982 SRP074888 RNA-Seq PAIRED
GSM2132566: STZ:T1D 2; Mus musculus; RNA-Seq
Sample: SRS1434278
BioProject: PRJNA321413
BioSample: SAMN04993347
Platform: ILLUMINA
Instrument: Illumina HiSeq 2000
Organism: Mus musculus
Sample attributes
source_name: Heart
strain: C57BL/6
tissue: Left Ventricle Heart
age: 12 weeks
treatment: STZ treatment: IP injection of 70mg/kg streptezotocin 1/per day for 5 days.
Original files (1)
Heart
Runs (1)
Run Spots Bases Size (MB) Files Link
SRR3499915 210702054 21070205400 12577.27 15_NoIndex_L002_R1_001.fastq.gz, 15_NoIndex_L002_R2_001.fastq.gz, SRR… SRA
SRX1757983 SRP074888 RNA-Seq PAIRED
GSM2132567: STZ:T1D 3; Mus musculus; RNA-Seq
Sample: SRS1434279
BioProject: PRJNA321413
BioSample: SAMN04993348
Platform: ILLUMINA
Instrument: Illumina HiSeq 2000
Organism: Mus musculus
Sample attributes
source_name: Heart
strain: C57BL/6
tissue: Left Ventricle Heart
age: 12 weeks
treatment: STZ treatment: IP injection of 70mg/kg streptezotocin 1/per day for 5 days.
Original files (1)
Heart
Runs (1)
Run Spots Bases Size (MB) Files Link
SRR3499916 191087435 19108743500 11087.36 24_NoIndex_L003_R1_001.fastq.gz, 24_NoIndex_L003_R2_001.fastq.gz, SRR… SRA

Linked Publications (1)

Dysregulation of RBFOX2 Is an Early Event in Cardiac Pathogenesis of Diabetes.
Cell reports · 2016

Data Files (5)

Accession File Name Stored Type Output Type Mapping Assembly Size Download
— 11_NoIndex_L001_R1_001.fastq.gz RNA-Seq 10.9 GB link
— 15_NoIndex_L002_R1_001.fastq.gz RNA-Seq 12.3 GB link
— 24_NoIndex_L003_R1_001.fastq.gz RNA-Seq 10.8 GB link
— 5407_NoIndex_L007_R1_001.fastq.gz RNA-Seq 12.3 GB link
— 5408_NoIndex_L008_R1_001.fastq.gz RNA-Seq 16.4 GB link