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Sample GSM1647361 Query DataSets for GSM1647361
Status Public on Jun 12, 2015
Title Mm_GFP_1.2x_IP_(20150213_13_2)
Sample type SRA
Source name Crosslinked MNase digested chromatin
Organism Mus musculus
Characteristics cell type: Mouse embryonic fibroblasts (MEFs)
transgene: GFP (negative control)
selection: size selected Ampure 1.2 vol
Extracted molecule genomic DNA
Extraction protocol Mouse embryonic fibroblasts (MEFs) were crosslinked using formaldehyde. Chromatin was fragmented using MNase and then sonicated to ensure complete extraction of chromatin and associated proteins. DNA was extracted from the solubilized chromatin and subjected to Solexa sequencing. After linker ligation, short insert lengths were enriched by recovering the unbound fraction from an Ampure bead selection using a volumetric ratio of DNA:beads of 1.2x.
Library strategy MNase-Seq
Library source genomic
Library selection MNase
Instrument model Illumina HiSeq 2500
Description MNase-seq size selected (1.2 vol Ampure). Mouse embryonic fibroblasts were crosslinked and the chromatin digested with micrococcal nuclease, followed by sequencing of the extracted DNA with an Ampure bead size selection.
Data processing 1. We used Bowtie2 (v2.2.1) with options "--no-unal --local --very-sensitive-local --no-discordant --no-mixed --contain --overlap --dovetail --phred33 -I 10 -X 700" to map paired-end 25bp reads to release mm9 of the M.musculus genomic sequence obtained from UCSC. 2. We extracted properly paired reads (Supplementary file .bed). 3. For each base pair in the genome, we counted the number of paired-end fragments aligned over it. 4. We normalized base pair counts by dividing by the total number of counts for all base pairs and then multiplying by the total number of base pairs in the genome (Supplementary file .wig)
Submission date Mar 31, 2015
Last update date May 15, 2019
Contact name Jorja Henikoff
Phone 206-667-4850
Organization name Fred Hutchinson Cancer Research Center
Department Basic Sciences
Lab Henikoff
Street address 1100 Fairview AV N, A1-162
City Seattle
State/province WA
ZIP/Postal code 98109-1024
Country USA
Platform ID GPL17021
Series (1)
GSE67454 A simple method for generating high-resolution maps of genome wide protein binding
BioSample SAMN03453192
SRA SRX974393
Named Annotation GSM1647361_Mm_GFP_1.2x_IP.wig.gz

Supplementary file Size Download File type/resource
GSM1647361_Mm_GFP_1.2x_IP.bed.gz 10.1 Mb (ftp)(http) BED
GSM1647361_Mm_GFP_1.2x_IP.wig.gz 523.2 Mb (ftp)(http) WIG
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file

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