|
| Status |
Public on Aug 10, 2013 |
| Title |
5hmC_ESC_shSuz12 |
| Sample type |
SRA |
| |
|
| Source name |
E14 embryonic stem cells transfected with shSuz12
|
| Organism |
Mus musculus |
| Characteristics |
cell line: E14 transfected with shSuz12
|
| 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 |
OTHER |
| Library source |
genomic |
| Library selection |
other |
| Instrument model |
Illumina HiScanSQ |
| |
|
| Data processing |
Library strategy: GLIB-Seq
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 files using a custom script
|
| |
|
| Submission date |
Feb 22, 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 (1) |
| GSE44566 |
Genome-wide analysis identifies a functional association of Tet1 and Polycomb PRC2 in mouse embryonic stem cells but not in differentiated tissues |
|
| Relations |
| SRA |
SRX244238 |
| BioSample |
SAMN01924341 |
