|
| Status |
Public on Feb 13, 2018 |
| Title |
PolII_WT_ChIPSeq |
| Sample type |
SRA |
| |
|
| Source name |
Mesenchymal stem/progenitor cells
|
| Organism |
Mus musculus |
| Characteristics |
cell type: BM-derived MSPCs
passages: 5-10
chip antibody: PolII (Abcam ab5095)
|
| 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 300 to 500 bp. Histone-DNA complexes were isolated with specific histone modification antibodies.
Illumina sequencing libraries were prepared from the ChIP and Input DNAs by the standard consecutive enzymatic steps of end-polishing, dA-addition, and adaptor ligation. After a final PCR amplification step, the resulting DNA libraries were quantified and sequenced.
|
| |
|
| Library strategy |
ChIP-Seq |
| Library source |
genomic |
| Library selection |
ChIP |
| Instrument model |
Illumina NextSeq 500 |
| |
|
| Data processing |
Basecalls performed using Illumina NextSeq 500
ChIP-Seq 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,aligned with no more than 2 mismatches,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: mm9
Supplementary_files_format_and_content: bigWig file
|
| |
|
| Submission date |
May 19, 2017 |
| Last update date |
May 15, 2019 |
| Contact name |
Feng-Chun Yang |
| E-mail(s) |
youngfaith28@gmail.com
|
| Organization name |
University of Miami Miller School of Medicine
|
| Lab |
Feng-Chun Yang
|
| Street address |
1011 NW 15th Street
|
| City |
Miami |
| State/province |
FL |
| ZIP/Postal code |
33136 |
| Country |
USA |
| |
|
| Platform ID |
GPL19057 |
| Series (1) |
| GSE99103 |
Loss of ASXL1 in the bone marrow niche dysregulates hematopoietic stem cell fates |
|
| Relations |
| BioSample |
SAMN07146776 |
| SRA |
SRX2837023 |
