|
| Status |
Public on Feb 10, 2015 |
| Title |
RRBS_shDnmt3b |
| Sample type |
SRA |
| |
|
| Source name |
ESC E14
|
| Organism |
Mus musculus |
| Characteristics |
treatment: shRNA Dnmt3b
cell type: embryonic stem cells
developmental stage: E14
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
Genomic DNA was extracted using DNeasy Blood and Tissue kit (Qiagen).
The genomic DNA was digested O/N with MspI (New England Biolabs). Libraries were generated with Illumina TruSeq DNA Sample Prep Kit following manufacturer instructions, bisulfite converted using EpiTect Bisulfite Kits (Qiagen) and sequenced on Illumina HiScanSQ Platform.
|
| |
|
| Library strategy |
Bisulfite-Seq |
| Library source |
genomic |
| Library selection |
Reduced Representation |
| Instrument model |
Illumina HiScanSQ |
| |
|
| Description |
DNA was treated with EpiTect Bisulfite Kits (Qiagen)
|
| Data processing |
Basecalls performed using CASAVA version 1.8
Nucleotide positions with a quality score behind 20 (Phred33 scale) were trimmed using the fastx_trimmer tool from the FASTX Toolkit
Reads were subjected to adapter clipping using the fastx_clipper tool from the FASTX Toolkit, and reads shorter than 35nt were discarded
Reads for RRBS_E14 were aligned to the mouse genome assembly using Bismark v0.10.1 using the default parameters
Methylation status was peformed using Methylation Extractor tool of Bismark.
Genome_build: mm9
Supplementary_files_format_and_content: bed file of RRBS were performed using custom perl script.
|
| |
|
| Submission date |
Mar 06, 2014 |
| 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) |
| GSE55659 |
Single base resolution analysis of 5-formyl and 5-carboxyl cytosine reveals the actual promoter DNA methylation dynamics in embryonic stem cells [RRBS] |
| GSE55660 |
Single base resolution analysis of 5-formyl and 5-carboxyl cytosine reveals the actual promoter DNA methylation dynamics in embryonic stem cells |
|
| Relations |
| BioSample |
SAMN02675495 |
| SRA |
SRX482063 |
| Named Annotation |
GSM1341320_RRBS_shDnmt3b.bed.gz |
