|
| Status |
Public on May 18, 2017 |
| Title |
MK1-input |
| Sample type |
SRA |
| |
|
| Source name |
Mouse keratinocyte cell-line 1
|
| Organism |
Mus musculus |
| Characteristics |
cell line: MK1
cell type: keratinocyte
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
Chromatin was extracted from mouse keratinocyte cells (MK1 and MK2) using a low SDS shearing kit (Diagenode: C01020010). Lysates were sonicated with a Bioruptor for 30-40 min. Ips were carried out with Indirect ChIP protocol using 4A4 antibody for p63 and histone antibodies from Diagenode.
Libraries were prepared using ThruPLEX DNA-seq kits from Rubicon Genomics. The samples were then 50 bp single-end sequenced on an Illumina HiSeq 2500.
|
| |
|
| Library strategy |
ChIP-Seq |
| Library source |
genomic |
| Library selection |
ChIP |
| Instrument model |
Illumina HiSeq 2500 |
| |
|
| Description |
Input ChIP DNA
UCSC/IGV track generated by merging MK1-Input and MK2-Input
processed data file: Mouse_Input.bigWig
|
| Data processing |
Raw sequencing reads were mapped to the Mus musculus genome (mm10 build) using Bowtie v1.1.1 with the following parameters: m = 1 (i.e. removes all those alignments with more than one match).
Pooled data files were generated using replicates with merge function in samtools v1.1
Genome_build: mm10
Supplementary_files_format_and_content: Bed and bigWig file for p63 ChIP-Seq.bigWig files for Histone ChIP-Seq
|
| |
|
| Submission date |
Sep 13, 2016 |
| Last update date |
May 15, 2019 |
| Contact name |
Satrajit Sinha |
| E-mail(s) |
[email protected]
|
| Phone |
716-881-7994
|
| Organization name |
State University of New York at Buffalo
|
| Department |
Department of Biochemistry
|
| Street address |
701 Ellicott Street
|
| City |
Buffalo |
| State/province |
NY |
| ZIP/Postal code |
14203 |
| Country |
USA |
| |
|
| Platform ID |
GPL17021 |
| Series (2) |
| GSE86900 |
Evolutionary re-wiring of p63 regulatory landscape has both epigenetic and transcriptomic implications and is the underlying cause for epidermal differences between mouse and human [ChIP-seq] |
| GSE86902 |
Evolutionary re-wiring of p63 regulatory landscape has both epigenetic and transcriptomic implications and is the underlying cause for epidermal differences between mouse and human |
|
| Relations |
| BioSample |
SAMN05770700 |
| SRA |
SRX2162795 |
