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GSE95156

GSE GEO Potentially related
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Pancreatic alpha and beta-cellular clocks have distinct molecular properties and impact on islet hormone secretion and gene expression

Organism: Mus musculus
Platform: GPL17021
Samples: 24
Experiment Types:
Expression profiling by high throughput sequencing
Submitted: Feb 21 2017
Last Updated: May 15 2019
Status: Public on Feb 22 2017
Contact: Celine,,Delucinge (University of Geneva)

Relations

BioProject: https://www.ncbi.nlm.nih.gov/bioproject/PRJNA376199 SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRP100479

Summary

We performed a parallel analysis of the molecular properties of α- and β-cell oscillators, using a mouse model expressing three reporter genes: one labeling α-cells, one specific for β-cells, and a third monitoring circadian gene expression. Diurnal transcriptome analysis in separated α- and β-cells revealed that a high number of genes with key roles in islet physiology, including regulators of glucose sensing and hormone secretion, are differentially expressed in these cell types. This study represents the first parallel large-scale circadian in vivo transcriptome analysis in separated α- and β-cells.

Overall Design

24 samples in duplicates (time course design)

Analysis (7 steps)

View Data Processing
Processing steps for GSE95156
  1. Sequenced paired-end reads were mapped to the whole genome (mm10) using STAR (Dobin et al., 2013) with default parameters.
  2. Genome index was built considering Ensembl annotation.
  3. For each Ensembl gene, all of the exons of the respective annotated protein-coding transcripts were considered.
  4. Reads up to one mismatch were counted considering only reads in the right gene orientation and mapped in the defined exons.
  5. Read counts were normalized by the library size (EdgeR, Robinson et al.
  6. 2010) and the average size of the transcripts.
  7. Normalized reads count (RPKM) were log2 transformed.

Supplementary Files (1)

GSE95156_Alpha_Beta.txt.gz Download
GEO Samples (24)
GSM2497927 GSM2497928 GSM2497929 GSM2497930 GSM2497931 GSM2497932 GSM2497933 GSM2497934 GSM2497935 GSM2497936 GSM2497937 GSM2497938 GSM2497939 GSM2497940 GSM2497941 GSM2497942 GSM2497943 GSM2497944 GSM2497945 GSM2497946 GSM2497947 GSM2497948 GSM2497949 GSM2497950

Dataset Citations (1)

PubMed citation (PMID 28275001)

SRA Experiments (24) and Runs (24)

Total: 29977 MB
SRX2581273 SRP100479 RNA-Seq PAIRED
GSM2497927: ZT8 beta_2; Mus musculus; RNA-Seq
Sample: SRS1995332
BioProject: PRJNA376199
BioSample: SAMN06365105
Platform: ILLUMINA
Instrument: Illumina HiSeq 2500
Organism: Mus musculus
Sample attributes
source_name: mouse beta cell
cell type: pancreatic beta cell
strain: triple reporter mouse
time: islet isolation time ZT8 (3PM)
Original files (1)
mouse beta cell
Runs (1)
Run Spots Bases Size (MB) Files Link
SRR5277343 22234694 2223469400 1336.35 ZT8b_2_GCCAAT_L003_R1_001.fastq.gz, ZT8b_2_GCCAAT_L003_R2_001.fastq.g… SRA
SRX2581274 SRP100479 RNA-Seq PAIRED
GSM2497928: ZT8 beta_1; Mus musculus; RNA-Seq
Sample: SRS1995334
BioProject: PRJNA376199
BioSample: SAMN06365104
Platform: ILLUMINA
Instrument: Illumina HiSeq 2500
Organism: Mus musculus
Sample attributes
source_name: mouse beta cell
cell type: pancreatic beta cell
strain: triple reporter mouse
time: islet isolation time ZT8 (3PM)
Original files (1)
mouse beta cell
Runs (1)
Run Spots Bases Size (MB) Files Link
SRR5277344 23381624 2338162400 1401.21 ZT8b_1_ACAGTG_L003_R1_001.fastq.gz, ZT8b_1_ACAGTG_L003_R2_001.fastq.g… SRA
SRX2581275 SRP100479 RNA-Seq PAIRED
GSM2497929: ZT8 alpha_2; Mus musculus; RNA-Seq
Sample: SRS1995331
BioProject: PRJNA376199
BioSample: SAMN06365102
Platform: ILLUMINA
Instrument: Illumina HiSeq 2500
Organism: Mus musculus
Sample attributes
source_name: mouse alpha cell
cell type: pancreatic alpha cell
strain: triple reporter mouse
time: islet isolation time ZT8 (3PM)
Original files (1)
mouse alpha cell
Runs (1)
Run Spots Bases Size (MB) Files Link
SRR5277345 22366138 2236613800 1316.4 ZT8a_2_ACTTGA_L001_R2_001.fastq.gz, SRR5277345, SRR5277345.sralite, Z… SRA
SRX2581276 SRP100479 RNA-Seq PAIRED
GSM2497930: ZT8 alpha_1; Mus musculus; RNA-Seq
Sample: SRS1995333
BioProject: PRJNA376199
BioSample: SAMN06365103
Platform: ILLUMINA
Instrument: Illumina HiSeq 2500
Organism: Mus musculus
Sample attributes
source_name: mouse alpha cell
cell type: pancreatic alpha cell
strain: triple reporter mouse
time: islet isolation time ZT8 (3PM)
Original files (1)
mouse alpha cell
Runs (1)
Run Spots Bases Size (MB) Files Link
SRR5277346 17062426 1706242600 1007.43 ZT8a_1_ATCACG_L001_R1_001.fastq.gz, ZT8a_1_ATCACG_L001_R2_001.fastq.g… SRA
SRX2581277 SRP100479 RNA-Seq PAIRED
GSM2497931: ZT4 beta_2; Mus musculus; RNA-Seq
Sample: SRS1995335
BioProject: PRJNA376199
BioSample: SAMN06365100
Platform: ILLUMINA
Instrument: Illumina HiSeq 2500
Organism: Mus musculus
Sample attributes
source_name: mouse beta cell
cell type: pancreatic beta cell
strain: triple reporter mouse
time: islet isolation time ZT4 (11AM)
Original files (1)
mouse beta cell
Runs (1)
Run Spots Bases Size (MB) Files Link
SRR5277347 20679474 2067947400 1238.74 SRR5277347, SRR5277347.sralite, ZT4b_2_ATTCCT_L002_R2_001.fastq.gz, Z… SRA
SRX2581278 SRP100479 RNA-Seq PAIRED
GSM2497932: ZT4 beta_1; Mus musculus; RNA-Seq
Sample: SRS1995336
BioProject: PRJNA376199
BioSample: SAMN06365099
Platform: ILLUMINA
Instrument: Illumina HiSeq 2500
Organism: Mus musculus
Sample attributes
source_name: mouse beta cell
cell type: pancreatic beta cell
strain: triple reporter mouse
time: islet isolation time ZT4 (11AM)
Original files (1)
mouse beta cell
Runs (1)
Run Spots Bases Size (MB) Files Link
SRR5277348 20137920 2013792000 1202.29 ZT4b_1_CGTACG_L002_R2_001.fastq.gz, SRR5277348, SRR5277348.sralite, Z… SRA
SRX2581279 SRP100479 RNA-Seq PAIRED
GSM2497933: ZT4 alpha_2; Mus musculus; RNA-Seq
Sample: SRS1995337
BioProject: PRJNA376199
BioSample: SAMN06365101
Platform: ILLUMINA
Instrument: Illumina HiSeq 2500
Organism: Mus musculus
Sample attributes
source_name: mouse alpha cell
cell type: pancreatic alpha cell
strain: triple reporter mouse
time: islet isolation time ZT4 (11AM)
Original files (1)
mouse alpha cell
Runs (1)
Run Spots Bases Size (MB) Files Link
SRR5277349 22397988 2239798800 1324.83 ZT4a_2_GTGAAA_L001_R1_001.fastq.gz, ZT4a_2_GTGAAA_L001_R2_001.fastq.g… SRA
SRX2581280 SRP100479 RNA-Seq PAIRED
GSM2497934: ZT4 alpha_1; Mus musculus; RNA-Seq
Sample: SRS1995338
BioProject: PRJNA376199
BioSample: SAMN06365096
Platform: ILLUMINA
Instrument: Illumina HiSeq 2500
Organism: Mus musculus
Sample attributes
source_name: mouse alpha cell
cell type: pancreatic alpha cell
strain: triple reporter mouse
time: islet isolation time ZT4 (11AM)
Original files (1)
mouse alpha cell
Runs (1)
Run Spots Bases Size (MB) Files Link
SRR5277350 18715132 1871513200 1095.27 ZT4a_1_CTTGTA_L001_R1_001.fastq.gz, ZT4a_1_CTTGTA_L001_R2_001.fastq.g… SRA
SRX2581281 SRP100479 RNA-Seq PAIRED
GSM2497935: ZT20 beta_2; Mus musculus; RNA-Seq
Sample: SRS1995340
BioProject: PRJNA376199
BioSample: SAMN06365098
Platform: ILLUMINA
Instrument: Illumina HiSeq 2500
Organism: Mus musculus
Sample attributes
source_name: mouse beta cell
cell type: pancreatic beta cell
strain: triple reporter mouse
time: islet isolation time ZT20 (3AM)
Original files (1)
mouse beta cell
Runs (1)
Run Spots Bases Size (MB) Files Link
SRR5277351 20157974 2015797400 1210.0 ZT20b_2_GGCTAC_L003_R1_001.fastq.gz, ZT20b_2_GGCTAC_L003_R2_001.fastq… SRA
SRX2581282 SRP100479 RNA-Seq PAIRED
GSM2497936: ZT20 beta_1; Mus musculus; RNA-Seq
Sample: SRS1995339
BioProject: PRJNA376199
BioSample: SAMN06365097
Platform: ILLUMINA
Instrument: Illumina HiSeq 2500
Organism: Mus musculus
Sample attributes
source_name: mouse beta cell
cell type: pancreatic beta cell
strain: triple reporter mouse
time: islet isolation time ZT20 (3AM)
Original files (1)
mouse beta cell
Runs (1)
Run Spots Bases Size (MB) Files Link
SRR5277352 22306231 2230623100 1336.94 SRR5277352, SRR5277352.sralite, ZT20b_1_TAGCTT_L003_R2_001.fastq.gz, … SRA
SRX2581283 SRP100479 RNA-Seq PAIRED
GSM2497937: ZT20 alpha_2; Mus musculus; RNA-Seq
Sample: SRS1995345
BioProject: PRJNA376199
BioSample: SAMN06365095
Platform: ILLUMINA
Instrument: Illumina HiSeq 2500
Organism: Mus musculus
Sample attributes
source_name: mouse alpha cell
cell type: pancreatic alpha cell
strain: triple reporter mouse
time: islet isolation time ZT20 (3AM)
Original files (1)
mouse alpha cell
Runs (1)
Run Spots Bases Size (MB) Files Link
SRR5277353 20456276 2045627600 1219.06 ZT20a_2_CCGTCC_L002_R1_001.fastq.gz, ZT20a_2_CCGTCC_L002_R2_001.fastq… SRA
SRX2581284 SRP100479 RNA-Seq PAIRED
GSM2497938: ZT20 alpha_1; Mus musculus; RNA-Seq
Sample: SRS1995341
BioProject: PRJNA376199
BioSample: SAMN06365094
Platform: ILLUMINA
Instrument: Illumina HiSeq 2500
Organism: Mus musculus
Sample attributes
source_name: mouse alpha cell
cell type: pancreatic alpha cell
strain: triple reporter mouse
time: islet isolation time ZT20 (3AM)
Original files (1)
mouse alpha cell
Runs (1)
Run Spots Bases Size (MB) Files Link
SRR5277354 21180511 2118051100 1243.52 SRR5277354, SRR5277354.sralite, ZT20a_1_CAGATC_L002_R2_001.fastq.gz, … SRA
SRX2581285 SRP100479 RNA-Seq PAIRED
GSM2497939: ZT16 beta_2; Mus musculus; RNA-Seq
Sample: SRS1995342
BioProject: PRJNA376199
BioSample: SAMN06365093
Platform: ILLUMINA
Instrument: Illumina HiSeq 2500
Organism: Mus musculus
Sample attributes
source_name: mouse beta cell
cell type: pancreatic beta cell
strain: triple reporter mouse
time: islet isolation time ZT16 (11PM)
Original files (1)
mouse beta cell
Runs (1)
Run Spots Bases Size (MB) Files Link
SRR5277355 23337558 2333755800 1392.51 ZT16b_2_ACTTGA_L003_R1_001.fastq.gz, ZT16b_2_ACTTGA_L003_R2_001.fastq… SRA
SRX2581286 SRP100479 RNA-Seq PAIRED
GSM2497940: ZT16 beta_1; Mus musculus; RNA-Seq
Sample: SRS1995343
BioProject: PRJNA376199
BioSample: SAMN06365092
Platform: ILLUMINA
Instrument: Illumina HiSeq 2500
Organism: Mus musculus
Sample attributes
source_name: mouse beta cell
cell type: pancreatic beta cell
strain: triple reporter mouse
time: islet isolation time ZT16 (11PM)
Original files (1)
mouse beta cell
Runs (1)
Run Spots Bases Size (MB) Files Link
SRR5277356 23374213 2337421300 1389.35 ZT16b_1_ATCACG_L003_R1_001.fastq.gz, SRR5277356, ZT16b_1_ATCACG_L003_… SRA
SRX2581287 SRP100479 RNA-Seq PAIRED
GSM2497941: ZT16 alpha_2; Mus musculus; RNA-Seq
Sample: SRS1995344
BioProject: PRJNA376199
BioSample: SAMN06365091
Platform: ILLUMINA
Instrument: Illumina HiSeq 2500
Organism: Mus musculus
Sample attributes
source_name: mouse alpha cell
cell type: pancreatic alpha cell
strain: triple reporter mouse
time: islet isolation time ZT16 (11PM)
Original files (1)
mouse alpha cell
Runs (1)
Run Spots Bases Size (MB) Files Link
SRR5277357 23801237 2380123700 1410.89 ZT16a_2_TGACCA_L002_R1_001.fastq.gz, ZT16a_2_TGACCA_L002_R2_001.fastq… SRA
SRX2581288 SRP100479 RNA-Seq PAIRED
GSM2497942: ZT16 alpha_1; Mus musculus; RNA-Seq
Sample: SRS1995346
BioProject: PRJNA376199
BioSample: SAMN06365090
Platform: ILLUMINA
Instrument: Illumina HiSeq 2500
Organism: Mus musculus
Sample attributes
source_name: mouse alpha cell
cell type: pancreatic alpha cell
strain: triple reporter mouse
time: islet isolation time ZT16 (11PM)
Original files (1)
mouse alpha cell
Runs (1)
Run Spots Bases Size (MB) Files Link
SRR5277358 22571822 2257182200 1326.83 ZT16a_1_CGATGT_L002_R1_001.fastq.gz, ZT16a_1_CGATGT_L002_R2_001.fastq… SRA
SRX2581289 SRP100479 RNA-Seq PAIRED
GSM2497943: ZT12 beta_2; Mus musculus; RNA-Seq
Sample: SRS1995348
BioProject: PRJNA376199
BioSample: SAMN06365089
Platform: ILLUMINA
Instrument: Illumina HiSeq 2500
Organism: Mus musculus
Sample attributes
source_name: mouse beta cell
cell type: pancreatic beta cell
strain: triple reporter mouse
time: islet isolation time ZT12 (7PM)
Original files (1)
mouse beta cell
Runs (1)
Run Spots Bases Size (MB) Files Link
SRR5277359 20272422 2027242200 1212.29 SRR5277359, ZT12b_2_GTGAAA_L003_R2_001.fastq.gz, ZT12b_2_GTGAAA_L003_… SRA
SRX2581290 SRP100479 RNA-Seq PAIRED
GSM2497944: ZT12 beta_1; Mus musculus; RNA-Seq
Sample: SRS1995347
BioProject: PRJNA376199
BioSample: SAMN06365088
Platform: ILLUMINA
Instrument: Illumina HiSeq 2500
Organism: Mus musculus
Sample attributes
source_name: mouse beta cell
cell type: pancreatic beta cell
strain: triple reporter mouse
time: islet isolation time ZT12 (7PM)
Original files (1)
mouse beta cell
Runs (1)
Run Spots Bases Size (MB) Files Link
SRR5277360 16292263 1629226300 975.32 ZT12b_1_CTTGTA_L003_R1_001.fastq.gz, SRR5277360, SRR5277360.sralite, … SRA
SRX2581291 SRP100479 RNA-Seq PAIRED
GSM2497945: ZT12 alpha_2; Mus musculus; RNA-Seq
Sample: SRS1995350
BioProject: PRJNA376199
BioSample: SAMN06365082
Platform: ILLUMINA
Instrument: Illumina HiSeq 2500
Organism: Mus musculus
Sample attributes
source_name: mouse alpha cell
cell type: pancreatic alpha cell
strain: triple reporter mouse
time: islet isolation time ZT12 (7PM)
Original files (1)
mouse alpha cell
Runs (1)
Run Spots Bases Size (MB) Files Link
SRR5277361 17575384 1757538400 1046.8 ZT12a_2_GGCTAC_L001_R1_001.fastq.gz, SRR5277361, ZT12a_2_GGCTAC_L001_… SRA
SRX2581292 SRP100479 RNA-Seq PAIRED
GSM2497946: ZT12 alpha_1; Mus musculus; RNA-Seq
Sample: SRS1995349
BioProject: PRJNA376199
BioSample: SAMN06365083
Platform: ILLUMINA
Instrument: Illumina HiSeq 2500
Organism: Mus musculus
Sample attributes
source_name: mouse alpha cell
cell type: pancreatic alpha cell
strain: triple reporter mouse
time: islet isolation time ZT12 (7PM)
Original files (1)
mouse alpha cell
Runs (1)
Run Spots Bases Size (MB) Files Link
SRR5277362 19536391 1953639100 1140.92 ZT12a_1_TAGCTT_L001_R1_001.fastq.gz, ZT12a_1_TAGCTT_L001_R2_001.fastq… SRA
SRX2581293 SRP100479 RNA-Seq PAIRED
GSM2497947: ZT0 beta_2; Mus musculus; RNA-Seq
Sample: SRS1995351
BioProject: PRJNA376199
BioSample: SAMN06365084
Platform: ILLUMINA
Instrument: Illumina HiSeq 2500
Organism: Mus musculus
Sample attributes
source_name: mouse beta cell
cell type: pancreatic beta cell
strain: triple reporter mouse
time: islet isolation time ZT0 (7AM)
Original files (1)
mouse beta cell
Runs (1)
Run Spots Bases Size (MB) Files Link
SRR5277363 20405993 2040599300 1221.18 SRR5277363.sralite, SRR5277363, ZT0b_2_GATCAG_L002_R2_001.fastq.gz, Z… SRA
SRX2581294 SRP100479 RNA-Seq PAIRED
GSM2497948: ZT0 beta_1; Mus musculus; RNA-Seq
Sample: SRS1995352
BioProject: PRJNA376199
BioSample: SAMN06365085
Platform: ILLUMINA
Instrument: Illumina HiSeq 2500
Organism: Mus musculus
Sample attributes
source_name: mouse beta cell
cell type: pancreatic beta cell
strain: triple reporter mouse
time: islet isolation time ZT0 (7AM)
Original files (1)
mouse beta cell
Runs (1)
Run Spots Bases Size (MB) Files Link
SRR5277364 20215041 2021504100 1220.76 ZT0b_1_TTAGGC_L002_R1_001.fastq.gz, ZT0b_1_TTAGGC_L002_R2_001.fastq.g… SRA
SRX2581295 SRP100479 RNA-Seq PAIRED
GSM2497949: ZT0 alpha_2; Mus musculus; RNA-Seq
Sample: SRS1995354
BioProject: PRJNA376199
BioSample: SAMN06365086
Platform: ILLUMINA
Instrument: Illumina HiSeq 2500
Organism: Mus musculus
Sample attributes
source_name: mouse alpha cell
cell type: pancreatic alpha cell
strain: triple reporter mouse
time: islet isolation time ZT0 (7AM)
Original files (1)
mouse alpha cell
Runs (1)
Run Spots Bases Size (MB) Files Link
SRR5277365 23497694 2349769400 1383.14 SRR5277365, SRR5277365.sralite, ZT0a_2_GCCAAT_L001_R2_001.fastq.gz, Z… SRA
SRX2581296 SRP100479 RNA-Seq PAIRED
GSM2497950: ZT0 alpha_1; Mus musculus; RNA-Seq
Sample: SRS1995353
BioProject: PRJNA376199
BioSample: SAMN06365087
Platform: ILLUMINA
Instrument: Illumina HiSeq 2500
Organism: Mus musculus
Sample attributes
source_name: mouse alpha cell
cell type: pancreatic alpha cell
strain: triple reporter mouse
time: islet isolation time ZT0 (7AM)
Original files (1)
mouse alpha cell
Runs (1)
Run Spots Bases Size (MB) Files Link
SRR5277366 22518490 2251849000 1324.89 ZT0a_1_ACAGTG_L001_R1_001.fastq.gz, ZT0a_1_ACAGTG_L001_R2_001.fastq.g… SRA

Potentially Related Publications (1)

This accession was text-mined from the PMC full text of these publications. It may be referenced for comparison or reused from another study rather than generated for them.

A role for alternative splicing in circadian control of exocytosis and glucose homeostasis.
Genes & development · 2020

Data Files (24)

Accession File Name Stored Type Output Type Mapping Assembly Size Download
— SRR5277347 RNA-Seq 1.2 GB link
— SRR5277352 RNA-Seq 1.3 GB link
— SRR5277354 RNA-Seq 1.2 GB link
— SRR5277359 RNA-Seq 1.2 GB link
— SRR5277363.sralite RNA-Seq 1.2 GB link
— SRR5277365 RNA-Seq 1.4 GB link
— ZT0a_1_ACAGTG_L001_R1_001.fastq.gz RNA-Seq 1.3 GB link
— ZT0b_1_TTAGGC_L002_R1_001.fastq.gz RNA-Seq 1.2 GB link
— ZT12a_1_TAGCTT_L001_R1_001.fastq.gz RNA-Seq 1.1 GB link
— ZT12a_2_GGCTAC_L001_R1_001.fastq.gz RNA-Seq 1.0 GB link
— ZT12b_1_CTTGTA_L003_R1_001.fastq.gz RNA-Seq 975.3 MB link
— ZT16a_1_CGATGT_L002_R1_001.fastq.gz RNA-Seq 1.3 GB link
— ZT16a_2_TGACCA_L002_R1_001.fastq.gz RNA-Seq 1.4 GB link
— ZT16b_1_ATCACG_L003_R1_001.fastq.gz RNA-Seq 1.4 GB link
— ZT16b_2_ACTTGA_L003_R1_001.fastq.gz RNA-Seq 1.4 GB link
— ZT20a_2_CCGTCC_L002_R1_001.fastq.gz RNA-Seq 1.2 GB link
— ZT20b_2_GGCTAC_L003_R1_001.fastq.gz RNA-Seq 1.2 GB link
— ZT4a_1_CTTGTA_L001_R1_001.fastq.gz RNA-Seq 1.1 GB link
— ZT4a_2_GTGAAA_L001_R1_001.fastq.gz RNA-Seq 1.3 GB link
— ZT4b_1_CGTACG_L002_R2_001.fastq.gz RNA-Seq 1.2 GB link
— ZT8a_1_ATCACG_L001_R1_001.fastq.gz RNA-Seq 1007.4 MB link
— ZT8a_2_ACTTGA_L001_R2_001.fastq.gz RNA-Seq 1.3 GB link
— ZT8b_1_ACAGTG_L003_R1_001.fastq.gz RNA-Seq 1.4 GB link
— ZT8b_2_GCCAAT_L003_R1_001.fastq.gz RNA-Seq 1.3 GB link