|
| Status |
Public on Sep 27, 2013 |
| Title |
Ezh2_ESC_shGFP |
| Sample type |
SRA |
| |
|
| Source name |
E14 embryonic stem cells, shGFP, Ezh2 ChIP
|
| Organism |
Mus musculus |
| Characteristics |
cell line: E14
cell type: embryonic stem cells
transfection: shGFP
chip antibody: Ezh2 (D2C9) (Cell Signaling, #5246)
|
| 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.
|
| |
|
| 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 |
SAMN02263949 |
| SRA |
SRX327699 |
