|
| Status |
Public on Jun 25, 2019 |
| Title |
Suz12_Mbd3KO_WT |
| Sample type |
SRA |
| |
|
| Source name |
Mbd3 Knock-out ESCs
|
| Organism |
Mus musculus |
| Characteristics |
gender: male
strain: 129SV
cell-type: embryonic stem cells
chip antibody: Suz12 (Millipore, 04-046)
|
| Growth protocol |
ESCs were culture under conventional ESC medium with LIF.
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
Lysates were clarified from sonicated nuclei and Suz12 were isolated with antibody.
Libraries were prepared from chromatin IP and input samples using the NEBNext ultra DNA library prep kit for Illumina (NEB # E7645S) and the NEBNext Multiplex Oligos for Illumina (NEB # E7335S), according to the manufacturers recommendations. The libraries were indexed and amplified using 8 PCR cycles, using the recommended conditions. After a final cleanup with Agencourt AmPure XP beads (Beckman # A63881), the library size distribution was confirmed by a BioAnalyzer 2100 (Agilent technologies) and quantified by the KAPA Library Quantification Kit (KAPA, Wilmington, MA), respectively. The final pools were prepared by mixing equimolar amounts of all individual indexed libraries and then sequenced on a NextSeq 500 (Illumina: Single-End 75).
|
| |
|
| Library strategy |
ChIP-Seq |
| Library source |
genomic |
| Library selection |
ChIP |
| Instrument model |
Illumina NextSeq 500 |
| |
|
| Data processing |
Basecalls performed using bcl2fastq2 version 2.18.0.12
Data were filtered by using FASTX Toolkit 0.0.1.3 (parameters -Q33 -q 20 -p 75)
ChIP-seq reads were aligned to the mm9 genome assembly using boetie2-2.2.5.
peaks were called using MACS2(q=0.001)
Ensembl Genes were defined using in GREAT (Two nearest genes association rules (within = five Kb) )
Genome_build: mm9
Supplementary_files_format_and_content: Peak file
|
| |
|
| Submission date |
Aug 14, 2017 |
| Last update date |
Jun 25, 2019 |
| Contact name |
Akihiko Okuda |
| E-mail(s) |
akiokuda@saitama-med.ac.jp
|
| Phone |
81-42-984-4787
|
| Organization name |
Saitama Medical University
|
| Department |
Research Center for Genomic Medicine
|
| Lab |
Division of Biomedical Sciences
|
| Street address |
1397-1 Yamane
|
| City |
Hidaka |
| State/province |
Saitama |
| ZIP/Postal code |
3501241 |
| Country |
Japan |
| |
|
| Platform ID |
GPL19057 |
| Series (1) |
| GSE102643 |
Identification of the coiled-coil domain as an essential element of MBD3 for preserving lineage commitment potential of ESCs |
|
| Relations |
| BioSample |
SAMN07504226 |
| SRA |
SRX3092213 |
