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Sample GSM1382276

Query DataSets for GSM1382276

Status

Public on May 08, 2014

Title

DHS-seq, 3T3-L1 4h (paired-end)

Sample type

SRA

Source name

3T3-L1 pre-adipocytes (4h)

Organism

Mus musculus

Characteristics

cell line: 3T3-L1
differentiation stage: pre-adipocytes
time: 4 hrs
treatment: DNase I treated

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.

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).

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.

Library strategy

DNase-Hypersensitivity

Library source

genomic

Library selection

DNAse

Instrument model

Illumina Genome Analyzer IIx

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.

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.

Submission date

May 07, 2014

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