Pjanic 2011, Nuclear Factor I binding site in WT and NFI-C KO MEFs.

Genome-wide map of Nuclear Factor I (NFI) binding sites in WT and NFI-C knock-out (NFI-C KO) mouse embryonic fibroblasts.

• Raw data was downloaded from: Provide the website and link to raw data
• Input file format: SRA, TXT, BED, ...
• Download date: DD-MM-YYYY

From M. musculus (July 2007 NCBI37/mm9).

ChIP-seq data:

	Filename	Description	Feature	GEO-ID
1	nf1_wt.sga	MEF|NFI|WT	NF-1	GSM398010
2	nf1_wt_rmsk.sga	MEF|NFI|WT|rmsk	NF-1	GSM398010
3	nf1_ko.sga	MEF|NFI|NFI-C KO	NFIC_KO	GSM398011
4	nf1_ko_rmsk.sga	MEF|NFI|NFI-C KO|rpmk	NFIC_KO	GSM398011
5	nf1_in.sga	MEF|Input|WT	INPUT	GSM398012
6	nf1_in_rmsk.sga	MEF|Input|WT|rmsk	INPUT	GSM398012

ChIP-seq peaks files:

	Filename	Description	Feature	GEO-ID
1	nf1_wt_peaks5_rmsk.sga	MEF|NFI|WT|5	NF-1_p	GSM398010
2	nf1_wt_peaks6_rmsk.sga	MEF|NFI|WT|6	NF-1_p	GSM398010
3	nf1_wt_peaks7_rmsk.sga	MEF|NFI|WT|7	NF-1_p	GSM398010
4	nf1_wt_peaks8_rmsk.sga	MEF|NFI|WT|8	NF-1_p	GSM398010

Notes on samples nomenclature:

• rmsk: samples were mapped using a repeat-masked version of mm9 genopme assembly
• peak files: peak files done using ChIP-Peak with different thresholds (5, 6, 7 and 8). 6th fieald in SGA file correspond to tag counts in peak area.

• Pjanic M, Pjanic P, Schmid C, Ambrosini G, Gaussin A, Plasari G, Mazza C, Bucher P, Mermod N
  Nuclear factor I revealed as family of promoter binding transcription activators. BMC Genomics. 2011 Apr 7;12:181. doi: 10.1186/1471-2164-12-181. 21473784
• Pjanic M, Schmid CD, Gaussin A, Ambrosini G, Adamcik J, Pjanic P, Plasari G, Kerschgens J, Dietler G, Bucher P, Mermod N
  Nuclear Factor I genomic binding associates with chromatin boundaries. BMC Genomics. 2013 Feb 12;14:99. doi: 10.1186/1471-2164-14-99. 23402308
• GEO series GSE15844: Genome-wide mapping of Nuclear Factor I binding sites using ChIP-Seq in WT and NFI-C knock-out MEFs