|
| Status |
Public on Nov 14, 2014 |
| Title |
SKO H3K36me3 (at 24 month age) rep2 |
| Sample type |
SRA |
| |
|
| Source name |
Hematopoietic stem cells (HSC)
|
| Organism |
Mus musculus |
| Characteristics |
cell type: Murine bone marrow derived primary HSCs
cell surface marker: SP-KSL-CD150+
strain: C57BL/6
chip antibody: Millipore 07-549
|
| Treatment protocol |
N/A
|
| Growth protocol |
N/A
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
Lysates were clarified from sonicated nuclei and histone-DNA complexes were isolated with antibody.
Genomic DNA were extracted from the cells and fragmented to 200-500 bp via biorupter. Followed by immunoprecipittaion with specific antibody, ChIPed DNA were successfully made library using ThruPLEX preparation kit without extra amplification (Rubicon, Ann Arbor, MI)
|
| |
|
| Library strategy |
ChIP-Seq |
| Library source |
genomic |
| Library selection |
ChIP |
| Instrument model |
Illumina HiSeq 2000 |
| |
|
| Description |
technical replicate of biological replicate 1
sko_H3K36me3.peaks.bed
|
| Data processing |
Basecalls performed using CASAVA version 1.4
ChIP-seq reads were aligned to the mm9 genome assembly using SOAP with 2 mismatches allowed; H3K4me3 and H3K36me3 are processed by MACS and H3K27me3 are processed by SICER for peak calling. Different replicates are accepted by the peak calling programs to generate one set of peaks for each condition.
Genome_build: mm9
Supplementary_files_format_and_content: BED format with 1-3 columns as chromosome, start, end. The 4th column for sicer.bed is read count. The 4th and 5th columns for peaks.bed are MACS peak id and pvalue.
|
| |
|
| Submission date |
Nov 13, 2014 |
| Last update date |
May 15, 2019 |
| Contact name |
deqiang sun |
| E-mail(s) |
dsun@tamu.edu
|
| Phone |
(713) 677-7439
|
| Organization name |
Texas A&M University
|
| Street address |
2121 W Holcombe Blvd
|
| City |
Houston |
| State/province |
TX |
| ZIP/Postal code |
77030 |
| Country |
USA |
| |
|
| Platform ID |
GPL13112 |
| Series (2) |
| GSE50793 |
Role of de novo DNA methyltransferases in hematopoietic stem cells |
| GSE63273 |
Role of de novo DNA methyltransferases in hematopoietic stem cells (ChIP-Seq) |
|
| Relations |
| BioSample |
SAMN03178033 |
| SRA |
SRX759251 |
