|
| Status |
Public on Feb 22, 2017 |
| Title |
Input-ChIP |
| Sample type |
SRA |
| |
|
| Source name |
Mouse embryonic fibroblasts
|
| Organism |
Mus musculus |
| Characteristics |
strain: C57BL/6
age: Embryos were isolated from the uteri at embryonic day 10.5.
antibody: none, Input
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
Lysates were clarified from sonicated nuclei and histone-DNA complexes were isolated with antibody.
Libraries were prepared according to Illumina's instructions. The libraries were sequenced on the Illumina Hiseq 2500 as single-end 50 base reads following Illumina's instructions.
|
| |
|
| Library strategy |
ChIP-Seq |
| Library source |
genomic |
| Library selection |
ChIP |
| Instrument model |
Illumina HiSeq 2500 |
| |
|
| Description |
Input fraction
|
| Data processing |
Image analysis and base calling were performed using RTA 1.17.20 and CASAVA 1.8.2. Sequence reads were mapped to reference genome mm9 using Bowtie 1.0.0 with the following parameters -m 1 --strata --best -y -S -l 40 -p 2. Heatmaps and quantitative comparisons of the ChIP-seq data were performed using seqMINER (http://bips.u-strasbg.fr/seqminer/).
Genome_build: mm9
Supplementary_files_format_and_content: To visualize peaks in the genome browser, we generated wig track files for each data set using WigMaker. Scores represent tag numbers per total uniquely mapped reads.
|
| |
|
| Submission date |
Feb 10, 2016 |
| Last update date |
May 15, 2019 |
| Contact name |
Christophe Papin |
| E-mail(s) |
papin@igbmc.fr
|
| Organization name |
IGBMC - CNRS UMR 7104 - Inserm U 964
|
| Street address |
1 rue Laurent Fries
|
| City |
ILLKIRCH-GRAFFENSTADEN |
| ZIP/Postal code |
67404 |
| Country |
France |
| |
|
| Platform ID |
GPL17021 |
| Series (2) |
| GSE66438 |
Combinatorial DNA methylation codes at repetitive elements |
| GSE77767 |
Combinatorial DNA methylation codes at repetitive elements [ChIP-Seq] |
|
| Relations |
| BioSample |
SAMN04482609 |
| SRA |
SRX1569734 |
