![](/coreweb/template1/pix/main_left_bg.gif) |
![](/coreweb/template1/pix/pixel.gif) |
GEO help: Mouse over screen elements for information. |
|
Status |
Public on Sep 06, 2016 |
Title |
RNA 12h glucose A |
Sample type |
SRA |
|
|
Source name |
β-cell_RNA 12h glucose
|
Organism |
Rattus norvegicus |
Characteristics |
cell line: INS-1E cell type: beta-cell
|
Treatment protocol |
Prior to exposure to high (25 mM) glucose, cells were preincubated with 5 mM glucose medium for 24 h. Time course experiments were performed in a reverse manner, i.e. medium was changed on all cells at time point 0 h, where after 25 mM glucose was added to the medium at consecutive time points and all cells were harvested at the 12 h time point.
|
Growth protocol |
INS-1E cells were cultured in RPMI 1640 w. 11 mM glucose supplemented with 5% Heat inactivated FCS, 50 uM β-MeOH, 1mM NaPyruvate, and 100 U/ml Penicilin + 100 mg/ml streptomycin. Cells were used between passages 60 and 90
|
Extracted molecule |
total RNA |
Extraction protocol |
Following Isol-RNA lysis Reagent® (5-Prime) extraction and EconoSpin (Epoc Life) column purification of total RNA, contaminant genomic DNA was removed from purified total RNA by TURBO® DNase digestion (Life Technologies), and ribosomal RNAs were removed using the Ribo-Zero® Human/Mouse/Rat kit (Epicentre). RNA fragmentation and cDNA synthesis was performed according to the manufacturers (Truseq 2® , Illumina) instructions. RNA-, DNase-, and ChIP-seq libraries were constructed using PentAdapters (Pentabase) essentially as previously described in (Nielsen R, Mandrup S, 2014, Methods in Enzymology 2014, Vol. 537, pp. 261-279).
|
|
|
Library strategy |
RNA-Seq |
Library source |
transcriptomic |
Library selection |
cDNA |
Instrument model |
Illumina HiSeq 1500 |
|
|
Description |
processed data file: Glucose_exon.txt, Glucose_intron.txt
|
Data processing |
alignment: RNA-seq reads were mapped to rn5 with STAR (Dobin, A., et al., Bioinformatics, 2013. 29(1): p. 15-21) using default parameters. quantification: Total RNA-seq coverage within introns of Ensembl (Rnor_5.0) genes were quantified using the iRNA-seq pipeline (Madsen et al, Nucl. Acids Res. 43 (6): e40), to asses primary transcript levels and in exons to asses mature transcript levels. edgeR normalized readcounts are provided in Glucose_intron.txt and Glucose_exon.txt Genome_build: rn5
|
|
|
Submission date |
May 19, 2016 |
Last update date |
May 15, 2019 |
Contact name |
Susanne Mandrup |
E-mail(s) |
s.mandrup@bmb.sdu.dk
|
Phone |
+45 6550 2340
|
Organization name |
University of Southern Denmark
|
Department |
Biochemistry and Molecular Biology
|
Street address |
Campusvej 55
|
City |
Odense M |
ZIP/Postal code |
5230 |
Country |
Denmark |
|
|
Platform ID |
GPL18404 |
Series (1) |
GSE81628 |
Integrative genomics outlines a biphasic glucose response and a ChREBP-RORγ axis regulating proliferation in β-cells |
|
Relations |
BioSample |
SAMN05019550 |
SRA |
SRX1774878 |
Supplementary data files not provided |
SRA Run Selector![Help](/coreweb/images/long_help4.gif) |
Raw data are available in SRA |
Processed data are available on Series record |
|
|
|
|
![](/coreweb/template1/pix/main_right_bg.gif) |