|
| Status |
Public on Jun 01, 2012 |
| Title |
Hematopoietic Stem Cell supernatant |
| Sample type |
SRA |
| |
|
| Source name |
Hematopoietic Stem Cell
|
| Organism |
Mus musculus |
| Characteristics |
cell type: Hematopoietic Stem Cell
genetic background: C57BL/6
gender: female
treatment: supernatant
|
| Treatment protocol |
After lysis of red cells in ACK lysing buffer (BioWhittaker®), approximately 109 cells were subjected to lineage depletion using the following rat anti-mouse antibodies: CD8a, CD4, CD11b, Ly-6G/Ly-6C, CD45R, and Ter119 (BD biosciences). Lineage negative cells (lin-) were stained with PE anti-mouse Sca1(clone D7) and APC anti-mouse CD117 (clone 2B8; BD biosciences). Lin- Sca-1+ c-kit+ (HSC; 1-2% of lineage depleted cells) and in- Sca-1- c-kit+ (CMP ;10% of lineage depleted cells) were sorted on a BD FACS Aria instrument.
|
| Growth protocol |
Hematopoietic stem cells and common myeloid progenitor cells were harvested from adult female C57BL/6 bone marrow.
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
Between 225 ng-540 ng of MBD2-enriched DNA and 1 ug of supernatant for each cell type were used to construct DNA libraries according to the Illumina protocol. The libraries were sequenced on the Illumina Genome Analyzer platform and 36 bp single-end reads were used to uniquely identify the MBD2-bound fraction of the mouse genome.
|
| |
|
| Library strategy |
MBD-Seq |
| Library source |
genomic |
| Library selection |
MBD2 protein methyl-CpG binding domain |
| Instrument model |
Illumina Genome Analyzer |
| |
|
| Description |
MBD2 Pulldown
|
| Data processing |
Sequenced reads were mapped to the mouse genome using the Eland short-read alignment program
Peaks for each cell-type were called using MACS, version 1.4, with a p-value threshold of p<10-5
Genome_build: UCSC assembly mm9, NCBI build 37
Supplementary_files_format_and_content: BED files were automatically generated by MACS, version 1.4
|
| |
|
| Submission date |
May 31, 2012 |
| Last update date |
May 15, 2019 |
| Contact name |
Jens Lichtenberg |
| E-mail(s) |
[email protected]
|
| Phone |
7402749495
|
| Fax |
3014024929
|
| Organization name |
National Institutes of Health
|
| Department |
National Human Genome Research Institute
|
| Street address |
49 Convent Dr 3A19
|
| City |
Bethesda |
| State/province |
MD |
| ZIP/Postal code |
20892 |
| Country |
USA |
| |
|
| Platform ID |
GPL9185 |
| Series (1) |
| GSE38354 |
Genome-Wide DNA Methylation Profiles in Hematopoietic Stem and Progenitor Cells Reveal Over-Representation of ETS Transcription Factor Binding Sites |
|
| Relations |
| SRA |
SRX150803 |
| BioSample |
SAMN01001251 |
