|
| Status |
Public on Feb 10, 2015 |
| Title |
ChIP-Seq_BioMock |
| Sample type |
SRA |
| |
|
| Source name |
ESC E14
|
| Organism |
Mus musculus |
| Characteristics |
ChIP: BirA cells (mock)
cell type: embryonic stem cells
developmental stage: E14
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
DNA was treated with EpiTect Bisulfite Kits (Qiagen)
Chromatin from fixed cells was extracted with 1% SDS buffer and sonicated for 20' prior immunoprecipiattion step (detailed description is in Material and Methods)
Library were perfomed using NEBNext ChIP-Seq Library Prep Master Mix Set (NEB), following manufacturer instructions
|
| |
|
| Library strategy |
ChIP-Seq |
| Library source |
genomic |
| Library selection |
ChIP |
| Instrument model |
Illumina HiScanSQ |
| |
|
| 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
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 file of BioTdg peaks
|
| |
|
| 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) |
| GSE55657 |
Single base resolution analysis of 5-formyl and 5-carboxyl cytosine reveals the actual promoter DNA methylation dynamics in embryonic stem cells [ChIP-Seq] |
| 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 |
SAMN02675492 |
| SRA |
SRX482053 |
