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| Status |
Public on Sep 06, 2016 |
| Title |
MED1 12h glucose A |
| Sample type |
SRA |
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| Source name |
β-cell_MED1 12h glucose
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| Organism |
Rattus norvegicus |
| Characteristics |
cell line: INS-1E
cell type: beta-cell
chip-antibody: anti-MED1 (M-255, sc-8998, Santa Cruz)
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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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| Description |
processed data file: MED1_peakfile.txt
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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: Mapped MED1 ChIP-seq reads were peak detected and quantified using HOMER (Heinz S, et al. 2010. Mol. Cell 38:576 –589). Tag directories were generated by calling makeTagDirectory (only including 1 tag pr bp, parameter: -tbp 1), and peak detection was performed on pooled libraries of replicate experiments using findPeaks -style factor (FDR ≤ 0. 1%). Individual MED1 peak files were subsequently merged using mergePeaks, and reads within 500 bp around the center of each peak were quantified for each replicate and each condition using annotatePeaks.pl. Peak locations and normalized counts (Pr. 10 M reads) for each condition and replicate are provided in MED1_peakfile.txt. 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 |
SAMN05019608 |
| SRA |
SRX1774910 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSM2159987_Med1.25mM.12h.A.bedGraph.gz |
31.9 Mb |
(ftp)(http) |
BEDGRAPH |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data provided as supplementary file |
| Processed data are available on Series record |
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