|
| Status |
Public on Jun 12, 2015 |
| Title |
Mm_GFP_1.1x_IP_(20150213_13) |
| 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 1.1 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 1.1x.
|
| |
|
| Library strategy |
MNase-Seq |
| Library source |
genomic |
| Library selection |
MNase |
| Instrument model |
Illumina HiSeq 2500 |
| |
|
| Description |
MNase-seq size selected (1.1 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 |
| E-mail(s) |
jorja@fhcrc.org
|
| 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 |
|
| Relations |
| BioSample |
SAMN03453191 |
| SRA |
SRX974392 |
| Named Annotation |
GSM1647360_Mm_GFP_1.1x_IP.wig.gz |
