|
| Status |
Public on Apr 24, 2010 |
| Title |
NFI ChIP-Seq 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: NFI (H300): sc-5567, SantaCruz Biotechnology
|
| 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 |
Chromatin IP against CTF/NFI (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
Please see 'readme.txt' for details about the additional processed data files: boundaries_closest_external_NFI_in_vivo_site.txt and boundaries_closest_internal_NFI_in_vivo_site.txt (8 txt files); NFI_peaks_wtMEF_300bpwindow_300bpvicinity_range.bed and sga (1 file each); miRNA_with_NFI_site (3 txt files).
|
| |
|
| 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 |
SRX017079 |
| BioSample |
SAMN00009373 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSM398010_H3K27me3_boundaries_closest_external_NFI_in_vivo_site.txt.gz |
315.8 Kb |
(ftp)(http) |
TXT |
| GSM398010_H3K27me3_boundaries_closest_internal_NFI_in_vivo_site.txt.gz |
312.5 Kb |
(ftp)(http) |
TXT |
| GSM398010_H3K36me3_boundaries_closest_external_NFI_in_vivo_site.txt.gz |
170.5 Kb |
(ftp)(http) |
TXT |
| GSM398010_H3K36me3_boundaries_closest_internal_NFI_in_vivo_site.txt.gz |
168.3 Kb |
(ftp)(http) |
TXT |
| GSM398010_H3K4me3_boundaries_closest_external_NFI_in_vivo_site.txt.gz |
334.5 Kb |
(ftp)(http) |
TXT |
| GSM398010_H3K4me3_boundaries_closest_internal_NFI_in_vivo_site.txt.gz |
335.7 Kb |
(ftp)(http) |
TXT |
| GSM398010_Lamina_boundaries_closest_external_NFI_in_vivo_site.txt.gz |
34.2 Kb |
(ftp)(http) |
TXT |
| GSM398010_Lamina_boundaries_closest_internal_NFI_in_vivo_site.txt.gz |
33.8 Kb |
(ftp)(http) |
TXT |
| GSM398010_NFI_peaks_wtMEF_300bpwindow_300bpvicinity_range.bed.gz |
299.8 Kb |
(ftp)(http) |
BED |
| GSM398010_NFI_peaks_wtMEF_300bpwindow_300bpvicinity_range.sga.gz |
215.7 Kb |
(ftp)(http) |
SGA |
| GSM398010_NFI_wtMEF_peaks.wig.gz |
2.2 Mb |
(ftp)(http) |
WIG |
| GSM398010_NFIchipseq_wild-typeMEF_ELAND_mapping.txt.gz |
342.7 Mb |
(ftp)(http) |
TXT |
| GSM398010_NFIchipseq_wtMEF_ELAND_mapping.sga.gz |
15.2 Mb |
(ftp)(http) |
SGA |
| GSM398010_miRNA_with_NFI_site_1kb_downstream.txt.gz |
221 b |
(ftp)(http) |
TXT |
| GSM398010_miRNA_with_NFI_site_1kb_upstream.txt.gz |
375 b |
(ftp)(http) |
TXT |
| GSM398010_miRNA_with_NFI_site_within_transcribed_region.txt.gz |
1.6 Kb |
(ftp)(http) |
TXT |
| GSM398010_readme.txt.gz |
1.2 Kb |
(ftp)(http) |
TXT |
SRA Run Selector |
| Processed data provided as supplementary file |
| Raw data are available in SRA |
