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Status |
Public on May 08, 2014 |
Title |
DHS-seq, 3T3-L1 4h (paired-end) |
Sample type |
SRA |
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Source name |
3T3-L1 pre-adipocytes (4h)
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Organism |
Mus musculus |
Characteristics |
cell line: 3T3-L1 differentiation stage: pre-adipocytes time: 4 hrs treatment: DNase I treated
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Treatment protocol |
3T3-L1 pre-adipocytes (day 0) were induced to differentiate using a cocktail of adipogenic inducers (1 μM dexamethasone, 0.5 mM 3-isobutyl-1-methylxantine, 1 μg/mL insulin, 10% FCS). Cells were harvested four hours after induction.
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Growth protocol |
3T3-L1 pre-adipocytes were maintained in DMEM supplemented with 10% calf serum. Two days post confluency (day 0), the cells were induced to differentiate using a cocktail of adipogenic inducers (1 μM dexamethasone, 0.5 mM 3-isobutyl-1-methylxantine, 1 μg/mL insulin, 10% FCS).
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Extracted molecule |
genomic DNA |
Extraction protocol |
DHS-seq libraries were constructed according to the manufacturer's instructions (Illumina) as described in (Nielsen R, Mandrup S, 2014 Genome-Wide Profiling of Transcription Factor Binding and Epigenetic Marks in Adipocytes by ChIP-seq. Methods in Enzymology 2014, Vol. 537, pp. 261-279). Nuclei isolated from 3T3-L1 cells four hours after induction of differentiation were subjected to DNase I digestion and small fragments were isolated by running the digested DNA through a sucrose gradient. DNA of approximately 100-150 bp were sequenced on the Illumina platform according to the instructions of the manufacturer. All this data comes from extensive sequencing of our previously published DHS-seq library (Siersbæk et al., 2011, EMBO J, 30(8):1459-72) and these data were therefore combined with our previously published data for downstream analyses, including identification of the DHS sites and footprints found here as processed data files.
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Library strategy |
DNase-Hypersensitivity |
Library source |
genomic |
Library selection |
DNAse |
Instrument model |
Illumina Genome Analyzer IIx |
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Description |
Nuclei isolated from 3T3-L1 cells four hours after induction of differentiation were subjected to DNase I digestion and small fragments were isolated by running the digested DNA through a sucrose gradient. DNA of approximately 100-150 bp were sequenced on the Illumina platform according to the instructions of the manufacturer. All this data comes from extensive sequencing of our previously published DHS-seq library (Siersbæk et al., 2011, EMBO J, 30(8):1459-72) and these data were therefore combined with our previously published data for downstream analyses, including identification of the DHS sites and footprints found here as processed data files.
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Data processing |
Using ultra deep sequencing of our previously published DHS-seq library (Siersbæk et al., 2011, EMBO J., 30(8):1459-72), we obtained 136.6 million mapped sequence tags. These were analyzed using our newly developed footprinting algorithm DNase2TF to obtain footprints of 8-30 bp (Myong-Hee Sung, Michael Guertin, Songjoon Baek, Gordon L. Hager, unpublished data). See Supplemental Experimental Methods for more details. Genome_build: mm9 Supplementary_files_format_and_content: BedGraph files were created using HOMER for visualization of DHS and cutcount profiles as well as expression data in the UCSC genome browser.
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Submission date |
May 07, 2014 |
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 |
GPL11002 |
Series (1) |
GSE57415 |
Molecular architecture of transcription factor hotspots in early adipogenesis |
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Relations |
BioSample |
SAMN02767371 |
SRA |
SRX535273 |
Supplementary data files not provided |
SRA Run Selector |
Raw data are available in SRA |
Processed data are available on Series record |
Processed data provided as supplementary file |
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