|
| Status |
Public on Aug 21, 2017 |
| Title |
7-minus-RRBS-39 |
| Sample type |
SRA |
| |
|
| Source name |
Hematopoietic progenitor cell
|
| Organism |
Mus musculus |
| Characteristics |
cell type: Mouse hematopoietic progenitor
time: D07
dox: minus
|
| Treatment protocol |
Human cell lines were treated with vitamin C in culture for 0, 12 and 72hrs. Mouse progenitors were treated with 1ug/ml Doxycycline to turn off Tet2 shRNA expression for 14 days
|
| Growth protocol |
Human cell lines were grown in RPMI media with 10-20% FBS, mouse progenitors were cultured in Optimem media supplemented with 10%FBS and SCF, IL3 and IL6 cytokines
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
DNA was isolated by proteinase K digestion, phenol chloroform extraction and ethanol precipitation
Bisulfite sequencing libraries were prepared using the TruMethyl-Seq Kit from CEGX following standard Illumina protocols
|
| |
|
| Library strategy |
Bisulfite-Seq |
| Library source |
genomic |
| Library selection |
Reduced Representation |
| Instrument model |
Illumina HiSeq 2500 |
| |
|
| Data processing |
Base calling and demultiplexing was performed using Illumina bcl2fastq software.
The sequencing reads were quality and adapter trimmed using Trim Galore with RRBS option.
The trimmed reads were aligned to the human and mouse genomes (build hg19/GRCh37 and mm10/GRCm38, respectively) using Bismark aligner.
Methylation calls were performed by Bismark.
Genome_build: hg19 and mm10
Supplementary_files_format_and_content: bismark coverage report (tab-delimited): <chromosome> <start position> <end position> <methylation percentage> <count methylated> <count unmethylated>
|
| |
|
| Submission date |
Jun 14, 2017 |
| Last update date |
May 15, 2019 |
| Contact name |
Igor Dolgalev |
| Organization name |
NYU Grossman School of Medicine
|
| Street address |
550 1st Ave
|
| City |
New York |
| State/province |
New York |
| ZIP/Postal code |
10016 |
| Country |
USA |
| |
|
| Platform ID |
GPL17021 |
| Series (2) |
| GSE97442 |
Genetic and pharmacological restoration of TET2 function blocks stem cell self-renewal and progression of leukemia |
| GSE100041 |
Reduced representation bisulfite-sequencing of human leukemia cells and mouse hematopoietic progenitors |
|
| Relations |
| BioSample |
SAMN07237929 |
| SRA |
SRX2918817 |
