|
| Status |
Public on Mar 03, 2017 |
| Title |
Cnt34 |
| Sample type |
SRA |
| |
|
| Source name |
Hematopoietic stem cell (HSC)
|
| Organism |
Mus musculus |
| Characteristics |
strain: C57BL/6
tissue: bone marrow
genotype: WT
cell type: HSC
cell markers: Lin-/c-Kit+/Sca-1+/Flk2-/CD48-/CD150+
|
| Treatment protocol |
FACS was used to isolate HSCs (Lin-/c-Kit+/Sca-1+/Flk2-/CD48-/CD150+) from mouse bone marrow
|
| Growth protocol |
Primary, uncultured cells
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
DNA was isolated from HSCs using the Qiagen Allprep kit
ERRBS libraries were prepared according to a previously published protocol (Akalin et al., PLoSGenetics, 2012) with modified size selection to accomadate the low amount of input DNA (see materials and methods).
|
| |
|
| Library strategy |
Bisulfite-Seq |
| Library source |
genomic |
| Library selection |
Reduced Representation |
| Instrument model |
Illumina HiSeq 2500 |
| |
|
| Data processing |
FASTQ files were generated by using the Illumina CASAVA 1.8.2 pipeline.
Adapter sequences were filtered out using the FAR software (Dodt, M, Ahmed R, Dieterich C. FAR -- flexible adapter remover. FAR project website (2011)) (http://sourceforge.net/projects/theflexibleadap/)
Reads were aligned to the mm10 genome using the bismark (http://www.bioinformatics.babraham.ac.uk/projects/bismark/) alignment tool.
Genome_build: mm10
Supplementary_files_format_and_content: The myCpG.txt is a tab-delimited text file that contains the location of the CpG, total read coverage on the C base, percentage of bisulfite-converted Cs (representing unmethylated Cs) and non-converted Cs (representing methylated Cs). The column headers are: chrBase, chr, base, strand, coverage, freqC, freqT.
|
| |
|
| Submission date |
May 21, 2016 |
| Last update date |
May 15, 2019 |
| Contact name |
Emmanuelle Passegue |
| E-mail(s) |
passeguee@stemcell.ucsf.edu
|
| Phone |
415-476-2426
|
| Organization name |
The Eli and Edythe Broad Center for Regenerative Medicine and Stem Cell Research, University of California San Francisco
|
| Department |
Department of Medicine, Hem/Onc Division
|
| Street address |
35 Medical Center Way, RMB-1017, Box 0667
|
| City |
San Francisco |
| State/province |
CA |
| ZIP/Postal code |
94143 |
| Country |
USA |
| |
|
| Platform ID |
GPL17021 |
| Series (2) |
| GSE81720 |
Autophagy maintains metabolism and functional activity of a subset of aged hematopoietic stem cells [RRBS] |
| GSE81721 |
Autophagy maintains metabolism and functional activity of a subset of aged hematopoietic stem cells |
|
| Relations |
| BioSample |
SAMN05161897 |
| SRA |
SRX1790722 |
