|
| Status |
Public on May 30, 2018 |
| Title |
CTCF ChIP-seq (p19 control) |
| Sample type |
SRA |
| |
|
| Source name |
mouse embryonic carcinoma cells
|
| Organism |
Mus musculus |
| Characteristics |
cell line: p19 cells
stable integrate: pBI-EGFP-FLAG-mCtcfl and pTA-N
treatment: Cells were kept in DMEM supplemented with 2 μg/ml Doxycycline, for induction the cells were grown for 48h in DMEM without Doxycycline
antibody: CTCF N2.2
|
| Treatment protocol |
For induction the cells were grown for 48h in DMEM without Doxycycline.
|
| Growth protocol |
Cells were kept in DMEM supplemented with 2 μg/ml Doxycycline.
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
Chromatin was isolated and sheared using BioRuptor (Diagenode). ChIPs were performed using a One-Day Protocol as described by Nelson et al. (2006 / Nature Protocols / DOI: 10.1038/nprot.2006.27
Sequencing libraries were prepared from 10 ng of immunoprecipitated DNA with the Illumina ChIPSeq DNA Sample Prep Kit according to Illuminas’ instructions
|
| |
|
| Library strategy |
ChIP-Seq |
| Library source |
genomic |
| Library selection |
ChIP |
| Instrument model |
Illumina HiSeq 2000 |
| |
|
| Description |
ChIP-seq
|
| Data processing |
Quality control of FASTQ files was done using FastQC.
Removal of low quality reads was done using fastx_toolkit-0.06
Reads were aligned to a pre-compiled index of the mouse hg19 genome using Bowtie (options: -k 1 -m 1) 0.12.5.
Duplicate reads were removed with Samtools' rmdup function.
Samtools was used to convert aligned reads to BAM format.
MACS 1.4 was used to call peaks at default settings
Genome_build: mm9
Supplementary_files_format_and_content: ChIP-seq peaks are supplied as BED and coverage vectors as bigwig files
|
| |
|
| Submission date |
Aug 28, 2017 |
| Last update date |
May 15, 2019 |
| Contact name |
Marek Bartkuhn |
| E-mail(s) |
marek.bartkuhn@gen.bio.uni-giessen.de
|
| Organization name |
Justus-Liebig-University Giessen
|
| Department |
Biomedical Informatics and Systems Medicine
|
| Street address |
Aulweg 132
|
| City |
Giessen |
| State/province |
Hessen |
| ZIP/Postal code |
35392 |
| Country |
Germany |
| |
|
| Platform ID |
GPL13112 |
| Series (2) |
|
| Relations |
| BioSample |
SAMN07568566 |
| SRA |
SRX3141583 |
