|
| Status |
Public on Sep 27, 2013 |
| Title |
MeDIP_shDnmt3L |
| Sample type |
SRA |
| |
|
| Source name |
ESC_shDnmt3L_MeDIP-seq
|
| Organism |
Mus musculus |
| Characteristics |
cell type: E14 embryonic stem cells
transfected with: shDnmt3L
enrichment method: Hydroxymethyl Collector (Active Motif)
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
Genomic DNA was extracted using DNeasy Blood and Tissue kit (Qiagen).
Genomic DNA was sonicated for 17' pulse 30"ON/30"OFF high with Bioruptor Twin (Diagenode). GLIB precipitation was performed using Hydroxymethyl Collector (Active Motif). Libraries were generated with ChIP-seq Sample Prep Kit (Illumina) and sequenced on Illumina HiScanSQ Platform.
|
| |
|
| Library strategy |
MeDIP-Seq |
| Library source |
genomic |
| Library selection |
5-methylcytidine antibody |
| Instrument model |
Illumina HiScanSQ |
| |
|
| Description |
Sample 2
|
| 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: mm9
Supplementary_files_format_and_content: bed files were generated from mapped SAM file using MACS for peak calling using a pvalue=1E-5
|
| |
|
| Submission date |
Feb 25, 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) |
| GSE44642 |
Dnmt3L-dependent regulation of DNA methylation promotes stem cells differentiation toward primitive germinal cells [MeDIP-seq] |
| GSE44644 |
Dnmt3L-dependent regulation of DNA methylation promotes stem cells differentiation toward primitive germinal cells |
|
| Relations |
| SRA |
SRX245529 |
| BioSample |
SAMN01924821 |
