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Sample GSM2159949

Query DataSets for GSM2159949

Status

Public on Sep 06, 2016

Title

RNA 1h glucose A

Sample type

SRA

Source name

β-cell_RNA 1h 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