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Status |
Public on Sep 06, 2016 |
Title |
Input 0h |
Sample type |
SRA |
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Source name |
β-cell_Input 0h
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Organism |
Rattus norvegicus |
Characteristics |
cell line: INS-1E cell type: beta-cell
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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.
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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
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Extracted molecule |
genomic DNA |
Extraction protocol |
ChIP experiments were performed according to standard protocol as described in (Siersbæk et al. 2012, MCB, 32: 3452-3463) 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).
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Library strategy |
ChIP-Seq |
Library source |
genomic |
Library selection |
ChIP |
Instrument model |
Illumina HiSeq 1500 |
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Data processing |
alignment: ChIP-seq reads were mapped to rn5 with STAR (Dobin, A., et al., Bioinformatics, 2013. 29(1): p. 15-21) set to not map across splice junctions (--alignIntronMax 1 --outSJfilterIntronMaxVsReadN 0) peakdetection, quantification and visualization: BedGraph files for visualization were generated using makeUCSCfile. Genome_build: rn5
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Submission date |
May 19, 2016 |
Last update date |
May 15, 2019 |
Contact name |
Susanne Mandrup |
E-mail(s) |
s.mandrup@bmb.sdu.dk
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Phone |
+45 6550 2340
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Organization name |
University of Southern Denmark
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Department |
Biochemistry and Molecular Biology
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Street address |
Campusvej 55
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City |
Odense M |
ZIP/Postal code |
5230 |
Country |
Denmark |
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Platform ID |
GPL18404 |
Series (1) |
GSE81628 |
Integrative genomics outlines a biphasic glucose response and a ChREBP-RORγ axis regulating proliferation in β-cells |
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Relations |
BioSample |
SAMN05019623 |
SRA |
SRX1774918 |
Supplementary file |
Size |
Download |
File type/resource |
GSM2159995_Input.5mM.bedGraph.gz |
30.4 Mb |
(ftp)(http) |
BEDGRAPH |
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Raw data are available in SRA |
Processed data provided as supplementary file |
Processed data are available on Series record |
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