|
Status |
Public on Apr 24, 2010 |
Title |
INPUT DNA in wild-type MEF |
Sample type |
SRA |
|
|
Source name |
mouse embryonic fibroblasts (MEF)
|
Organism |
Mus musculus |
Characteristics |
strain: C57BL/6 passages: 6-7 chip antibody: no antibody
|
Growth protocol |
Mouse embryonic fibroblasts were extracted from mouse embryos of 14.5 days. Cells from WT (wild-type) and NFI-C knock-out embryos were cultured under the following conditions: 37°C, 5% CO2, DMEM (GIBCO, 41966), Supplementary 10% FBS (GIBCO, Fetal Bovine Serum, qualified origin US, 26140-079), 1% v/v nonessential amino-acids (GIBCO, 11140-035), 1% v/v L-glutamine (GIBCO, 25030-024).
|
Extracted molecule |
genomic DNA |
Extraction protocol |
Chromatin was extracted from approximately 20,000,000 cultured MEFs and cross-linked using 11% formaldehyde. Extracted chromatin was fragmented to the average fragment size of 1000bp using high-frequency sound sonication on VibraCell-75455 (Bioblock Scientific). ChIP was performed using the commercial antibody against NFI group of proteins (NFI (H300): sc-5567, SantaCruz Biotechnology). Antibody complexes were precipitated using rProtein A Sepharose Fast Flow (Amersham Biosciences). ChIP DNA was processed using the contents of the ChIP-Seq Sample Prep Kit (Illumina). Size range of templates was selected by loading the entire processed sample on a 2% agarose gel and excising the gel region of 50-400bp. PCR amplification of the gel-extracted DNA was performed for 18 cycles using adapter-specific primers. Each sample was loaded into 3 separate flow cell channels of the Illumina Cluster Station and then subjected to sequencing-by-synthesis on the Illumina Genome Analyzer sequencing system.
|
|
|
Library strategy |
ChIP-Seq |
Library source |
genomic |
Library selection |
ChIP |
Instrument model |
Illumina Genome Analyzer |
|
|
Description |
Non-precipitated genomic DNA (wild-type MEF)
|
Data processing |
Obtained sequence tags were aligned to the reference mouse genome (mm9) using Illumina ELAND software. Clustering and correlation analyses of mapped reads were performed using ChIP-peak and ChIP-cor tools available on the ChIP-Seq Analysis Server (http://www.isrec.isb-sib.ch/chipseq/). In vivo NFI sites were defined using the ChIP-peak tool and applying the following parameters: window width - 1000bp, vicinity range - 1bp, peak threshold - 5 tags, count cut-off - 1 tag, centering - 75bp (for visualization in UCSC Genome browser: upload corresponding peaks.wig files).
File formats described at http://www.isrec.isb-sib.ch/chipseq/sga_specs.html
|
|
|
Submission date |
Apr 27, 2009 |
Last update date |
May 15, 2019 |
Contact name |
Milos Pjanic |
E-mail(s) |
milos.pjanic@unil.ch
|
Phone |
+41 21 693 61 48
|
Fax |
+41 21 693 76 10
|
Organization name |
Faculty of Biology and Medicine, University of Lausanne
|
Department |
Institute of Biotechnology
|
Lab |
Laboratory of Molecular Biotechnology
|
Street address |
EPFL CH B1 426 Station 6
|
City |
Lausanne |
State/province |
VD |
ZIP/Postal code |
1015 |
Country |
Switzerland |
|
|
Platform ID |
GPL9185 |
Series (1) |
GSE15844 |
Genome-wide mapping of Nuclear Factor I binding sites using ChIP-Seq in WT and NFI-C knock-out MEFs |
|
Relations |
SRA |
SRX017081 |
BioSample |
SAMN00009375 |