|
| Status |
Public on Mar 05, 2014 |
| Title |
BioMyc_ChIPSeq |
| Sample type |
SRA |
| |
|
| Source name |
ESC E14
|
| Organism |
Mus musculus |
| Characteristics |
cell line background: E14
cell type: embryonic stem cells (ESCs)
genotype/variation: a stable clone (of E14 mESCs) expressing Biotin-tagged Myc
chip antibody: Dynabeads MyOneTM Streptavidin T1
chip antibody vendor: Invitrogen
chip antibody cat. #: 65601
|
| 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 |
SAMN02209995 |
| SRA |
SRX312227 |
