← All datasets

GSE92602

GSE GEO
View on GEO Export SRA CSV

Identification of islet-enriched long non-coding RNAs contributing to beta-cell failure in type 2 diabetes

Organism: Mus musculus
Platform: GPL9250
Samples: 6
Experiment Types:
Expression profiling by high throughput sequencing
Submitted: Dec 19 2016
Last Updated: May 15 2019
Status: Public on Sep 07 2017
Contact: Frederic,,Burdet (Swiss Institute of Bioinformatics)

Relations

BioProject: https://www.ncbi.nlm.nih.gov/bioproject/PRJNA358100 SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRP095370

Summary

To study the contribution of long non-coding RNAs (lncRNAs) to beta-cell failure and the development of type 2 diabetes, we used RNA-sequencing coupled with de novo annotation to search for novel transcripts dysregulated in islets of diet-induced obese mice. We identified about 1500 novel lncRNAs, a number of which were differentially expressed in obese mice. The expression of two lncRNAs highly enriched in beta-cells, βlinc2 and βlinc3, correlated to body weight gain and glycaemia levels in obese mice and was also modified in diabetic db/db mice. The expression of both lncRNAs was also modulated in vitro in isolated islets cells by glucolipotoxic conditions. Moreover, the expression of the human orthologue of βlinc3 was altered in the islets of type 2 diabetic patients and was associated to the BMI of the donors. Modulation of the level of βlinc2 and βlinc3 by overexpression or downregulation in MIN6 and mouse islets cells, did not affect insulin secretion but increased beta-cell apoptosis. Taken together, the data show that lncRNAs are modulated in a model of obesity-associated type 2 diabetes and that variations in the expression of some of them may contribute to beta-cell failure during the development of the disease.

Overall Design

Performed RNA sequencing coupled with de novo annotation to search for known (protein and long non coding RNAs) and novel transcripts (lncRNAs) dysregulated in pancreatic islets of diet-induced obesity mice versus mice fed a normal diet. (C57BL/6 mice 14 weeks old at sacrifice, fed for 8 weeks)

Analysis (5 steps)

View Data Processing
Processing steps for GSE92602
  1. Base calling was with Illumina GAP Pipeline Software v1.90
  2. Sequences were aligned to mm9 reference genome using Tophat 2.0.8 with option -g with mm9 reference GTF
  3. Novel transcripts were predicted with Cufflinks 2.1.1
  4. Novel transcripts predictions were merged with mm9 reference genome using Cuffmerge 2.1.1 with option -G with mm9 reference GTF
  5. Counts were generated using htseq-count v0.5.4p3

Supplementary Files (5)

GSE92602_Differential_Expression_Results_HFD_vs_ND.xlsx Download
GSE92602_Novel_transcripts.xlsx Download
GSE92602_mouse_genes_counts_normalized.txt.gz Download
GSE92602_raw_counts.txt.gz Download
GSE92602_transcripts.gtf.gz Download
GEO Samples (6)

Dataset Citations (1)

SRA Experiments (6) and Runs (6)

Total: 209124 MB
SRX2436335 SRP095370 RNA-Seq PAIRED
GSM2433300: normal diet 1; Mus musculus; RNA-Seq
Sample: SRS1871339
BioProject: PRJNA358100
BioSample: SAMN06166438
Platform: ILLUMINA
Instrument: Illumina Genome Analyzer II
Organism: Mus musculus
Sample attributes
source_name: pancreatic islets
strain: C57BL/6
age: 14 weeks
tissue: pancreatic islets
diet: normal
Original files (1)
pancreatic islets
Runs (1)
Run Spots Bases Size (MB) Files Link
SRR5121119 286424104 57857669008 35084.78 ND1_L7_R2.fq.gz, SRR5121119, SRR5121119.sralite, ND1_L7_R1.fq.gz SRA
SRX2436336 SRP095370 RNA-Seq PAIRED
GSM2433301: normal diet 2; Mus musculus; RNA-Seq
Sample: SRS1871340
BioProject: PRJNA358100
BioSample: SAMN06166437
Platform: ILLUMINA
Instrument: Illumina Genome Analyzer II
Organism: Mus musculus
Sample attributes
source_name: pancreatic islets
strain: C57BL/6
age: 14 weeks
tissue: pancreatic islets
diet: normal
Original files (1)
pancreatic islets
Runs (1)
Run Spots Bases Size (MB) Files Link
SRR5121120 305194447 61649278294 34105.79 ND2_L5_R1.fq.gz, ND2_L5_R2.fq.gz, SRR5121120, SRR5121120.sralite SRA
SRX2436337 SRP095370 RNA-Seq PAIRED
GSM2433302: normal diet 3; Mus musculus; RNA-Seq
Sample: SRS1871341
BioProject: PRJNA358100
BioSample: SAMN06166436
Platform: ILLUMINA
Instrument: Illumina Genome Analyzer II
Organism: Mus musculus
Sample attributes
source_name: pancreatic islets
strain: C57BL/6
age: 14 weeks
tissue: pancreatic islets
diet: normal
Original files (1)
pancreatic islets
Runs (1)
Run Spots Bases Size (MB) Files Link
SRR5121121 324122784 65472802368 38840.88 ND3_L6_R2.fq.gz, SRR5121121.sralite, SRR5121121, ND3_L6_R1.fq.gz SRA
SRX2436338 SRP095370 RNA-Seq PAIRED
GSM2433303: high fat diet 1; Mus musculus; RNA-Seq
Sample: SRS1871342
BioProject: PRJNA358100
BioSample: SAMN06166435
Platform: ILLUMINA
Instrument: Illumina Genome Analyzer II
Organism: Mus musculus
Sample attributes
source_name: pancreatic islets
strain: C57BL/6
age: 14 weeks
tissue: pancreatic islets
diet: high fat
Original files (1)
pancreatic islets
Runs (1)
Run Spots Bases Size (MB) Files Link
SRR5121122 281803734 56924354268 34716.34 SRR5121122.sralite, SRR5121122, HDR1_L4_R2.fq.gz, HDR1_L4_R1.fq.gz SRA
SRX2436339 SRP095370 RNA-Seq PAIRED
GSM2433304: high fat diet 2; Mus musculus; RNA-Seq
Sample: SRS1871344
BioProject: PRJNA358100
BioSample: SAMN06166434
Platform: ILLUMINA
Instrument: Illumina Genome Analyzer II
Organism: Mus musculus
Sample attributes
source_name: pancreatic islets
strain: C57BL/6
age: 14 weeks
tissue: pancreatic islets
diet: high fat
Original files (1)
pancreatic islets
Runs (1)
Run Spots Bases Size (MB) Files Link
SRR5121123 260802628 52682130856 31768.09 SRR5121123.sralite, SRR5121123, HDR2_L5_R2.fq.gz, HDR2_L5_R1.fq.gz SRA
SRX2436340 SRP095370 RNA-Seq PAIRED
GSM2433305: high fat diet 3; Mus musculus; RNA-Seq
Sample: SRS1871343
BioProject: PRJNA358100
BioSample: SAMN06166433
Platform: ILLUMINA
Instrument: Illumina Genome Analyzer II
Organism: Mus musculus
Sample attributes
source_name: pancreatic islets
strain: C57BL/6
age: 14 weeks
tissue: pancreatic islets
diet: high fat
Original files (1)
pancreatic islets
Runs (1)
Run Spots Bases Size (MB) Files Link
SRR5121124 281322721 56827189642 34607.99 HDR3_L6_R1.fq.gz, HDR3_L6_R2.fq.gz, SRR5121124.sralite, SRR5121124 SRA

Linked Publications (1)

Data Files (6)

Accession File Name Stored Type Output Type Mapping Assembly Size Download
HDR3_L6_R1.fq.gz RNA-Seq 33.8 GB link
ND1_L7_R2.fq.gz RNA-Seq 34.3 GB link
ND2_L5_R1.fq.gz RNA-Seq 33.3 GB link
ND3_L6_R2.fq.gz RNA-Seq 37.9 GB link
SRR5121122.sralite RNA-Seq 33.9 GB link
SRR5121123.sralite RNA-Seq 31.0 GB link