|
Status |
Public on Sep 27, 2013 |
Title |
BioDnmt3L_ESC_shSuz12 |
Sample type |
SRA |
|
|
Source name |
E14-BioDnmt3L embryonic stem cells, shSuz12, Dnmt3L ChIP
|
Organism |
Mus musculus |
Characteristics |
cell line: E14 cell type: embryonic stem cells genotype/variation: BioDnmt3L transfection: shSuz12 chip antibody: Dynabeads MyOne Streptavidin T1 (Invitrogen, #65601)
|
Extracted molecule |
genomic DNA |
Extraction protocol |
Chromatin from fixed cells was extracted with 1% SDS buffer and sonicated for 20' prior to immunoprecipitation step (detailed description is in Material and Methods of manuscript). Library were performed using ChIP-Seq Sample Prep Kit from Illumina.
|
|
|
Library strategy |
ChIP-Seq |
Library source |
genomic |
Library selection |
ChIP |
Instrument model |
Illumina HiScanSQ |
|
|
Description |
Chromatin
|
Data processing |
Basecalls performed using CASAVA version 1.8. ChIP-seq reads were aligned to the mm9 genome assembly using Bowtie v0.12.7 using the following parameters : -q --max /dev/null -v 1 -S --sam-nohead -m 1. Data were filtered using the following specifications: duplicate reads were filtered out. Peaks were called using MACS v1.4.1 with the following setting: --gsize=mm --nolambda --bw=300. Genome_build: MGSCv37 Supplementary_files_format_and_content: Bed files were generated from mapped SAM file using MACS software.
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|
|
Submission date |
Jul 24, 2013 |
Last update date |
May 15, 2019 |
Contact name |
Francesco Neri |
E-mail(s) |
francesco.neri@unito.it
|
Organization name |
University of Torino
|
Street address |
Via Nizza 52
|
City |
Torino |
State/province |
Italy |
ZIP/Postal code |
10126 |
Country |
Italy |
|
|
Platform ID |
GPL16173 |
Series (2) |
GSE44644 |
Dnmt3L-dependent regulation of DNA methylation promotes stem cells differentiation toward primitive germinal cells |
GSE49178 |
Dnmt3L-dependent regulation of DNA methylation promotes stem cells differentiation toward primitive germinal cells [ChIP-seq] |
|
Relations |
BioSample |
SAMN02263951 |
SRA |
SRX327702 |