|
| Status |
Public on Feb 13, 2018 |
| Title |
Tet2_MSC_KO_1_5-hmC |
| Sample type |
SRA |
| |
|
| Source name |
Mesenchymal stem/progenitor cells
|
| Organism |
Mus musculus |
| Characteristics |
tissue: bone marrow
cell type: mesenchymal stem/progenitor cells
strain: C57BL/6
passages: 5-10
genotype: Tet2-/-
|
| Growth protocol |
Bone marrow–derived mesenchymal stem/progenitor cells were cultured with MSC medium (MesenCult basal media plus 20% of MesenCult Supplemental), and replated when the cultures reached 80-90% confluency.
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
MSPCs were fixed with 1% formaldehyde, lysates were sonicated and the DNA was sheared to an average length of 100 to 500 bp. 5hmC-DNA complexes were isolated with biotin.
Enriched DNA from hME-seal were subjected to library construction using the NEBNext ChIP-Seq Library Prep Reagent Set for Illumina according to the manufacturer’s protocol.
|
| |
|
| Library strategy |
OTHER |
| Library source |
genomic |
| Library selection |
other |
| Instrument model |
Illumina HiSeq 2500 |
| |
|
| Description |
Genome-wide 5hmc Profiling (hME-Seal) using isolation with biotin
|
| Data processing |
Library strategy: hME-SEAL
Basecalls performed using Illumina HISeq 2500.
reads were aligned to the mm10 genome assembly using the BWA algorithm with default settings.
Data were filtered using the following specifications:only reads that pass Illumina's purity filter, and map uniquely to the genome were used in the subsequent analysis,than duplicate reads were removed.
peaks were called using MACS version 2.1.1 with default setting.
Genome_build: mm10
Supplementary_files_format_and_content: bigWig file
|
| |
|
| Submission date |
Jun 15, 2017 |
| Last update date |
May 15, 2019 |
| Contact name |
Rong Li |
| E-mail(s) |
pumclirong@163.com
|
| Organization name |
Chinese Academy of Medical Sciences and Peking Union Medical College
|
| Department |
Institute of Hematology and Blood Diseases Hospital
|
| Lab |
State Key Laboratory of Experimental Hematology
|
| Street address |
No.288, Nanjing Road,Heping District
|
| City |
Tianjin |
| State/province |
Tianjin |
| ZIP/Postal code |
300020 |
| Country |
China |
| |
|
| Platform ID |
GPL17021 |
| Series (2) |
| GSE100072 |
Tet2 loss dysregulates the behavior of bone marrow derived mesenchymal stromal cells [hME-Seal] |
| GSE100073 |
Tet2 loss dysregulates the behavior of bone marrow derived mesenchymal stromal cells |
|
| Relations |
| BioSample |
SAMN07246943 |
| SRA |
SRX2922221 |
