|
Status |
Public on Mar 05, 2014 |
Title |
IgG_ChIPSeq |
Sample type |
SRA |
|
|
Source name |
ESC E14
|
Organism |
Mus musculus |
Characteristics |
cell line background: E14 cell type: embryonic stem cells (ESCs) genotype/variation: parental wild type chip antibody: anti-IgG chip antibody vendor: santa cruz biotechnology chip antibody cat. #: sc2027
|
Extracted molecule |
genomic DNA |
Extraction protocol |
Chromatin was extracted from crosslinked cells using SDS lysis buffer. Chromatin was immunoprecipiate with specific beads and DNA was eluted and de-crosslinked.
|
|
|
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 -p 1e-8 Genome_build: mm9 Supplementary_files_format_and_content: BED files of bound regions were calculated using MACS with respective control (biomock for bioMyc and IgG for Max) at pvalue 1E-8
|
|
|
Submission date |
Jun 20, 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) |
GSE48175 |
Identification of Myc and Max genomic targets in mouse embryonic stem cells. |
|
Relations |
BioSample |
SAMN02209997 |
SRA |
SRX312230 |