|
| Status |
Public on Aug 13, 2018 |
| Title |
MDS-L_MOCK-Input |
| Sample type |
SRA |
| |
|
| Source name |
MDS-L
|
| Organism |
Homo sapiens |
| Characteristics |
tissue: myelodysplastic syndrome (MDS) cell line MDS-L
transduction: MOCK vector
antibody: input
|
| Treatment protocol |
Lentivirous base transduction of SIRT1 overexpression or MOCK vector
|
| Growth protocol |
RPMI 1640 medium with 10% FBS and 1% penicillin-streptomycin in the presence of 30 ng/mL human recombinant human IL-3
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
Genomic DNA were sonicated and enriched with anti-5hmC antibody.
KAPA HyperPrep Kits
|
| |
|
| Library strategy |
MeDIP-Seq |
| Library source |
genomic |
| Library selection |
5-methylcytidine antibody |
| Instrument model |
Illumina HiSeq 2500 |
| |
|
| Data processing |
Illumina bcl2fastq2-2.18 software was used for basecalling
Sequencing reads were aligned to the human genome build GRCh37/hg19 using theBurrows-Wheeler Aligner (BWA, v0.7.5a) (Li and Durbin, 2009).
MACS2 was utilized to define peaks with significantly enriched signals (Zhang et al., 2008).
|
| |
|
| Submission date |
Jul 19, 2018 |
| Last update date |
Aug 14, 2018 |
| Contact name |
Sun Jie |
| E-mail(s) |
[email protected]
|
| Organization name |
City of Hope
|
| Lab |
Li Lab
|
| Street address |
1500 East Duarte Road
|
| City |
Duarte |
| State/province |
CA |
| ZIP/Postal code |
91010 |
| Country |
USA |
| |
|
| Platform ID |
GPL16791 |
| Series (2) |
| GSE117363 |
SIRT1 Activation Disrupts Maintenance of Myelodysplastic Syndrome Stem and Progenitor Cells by Restoring TET2 Function [hMeDIP-Seq] |
| GSE117383 |
SIRT1 Activation Disrupts Maintenance of Myelodysplastic Syndrome Stem and Progenitor Cells by Restoring TET2 Function |
|
| Relations |
| BioSample |
SAMN09691764 |
| SRA |
SRX4408478 |
