|
| Status |
Public on Jun 30, 2024 |
| Title |
4T1 control replicate 3 [RRBS] |
| Sample type |
SRA |
| |
|
| Source name |
4T1
|
| Organism |
Mus musculus |
| Characteristics |
cell line: 4T1
|
| Treatment protocol |
B16F10 and 4T1 cells (2x10^4/well in 24 well plates) were treated with 0.1 uM or 1 uM of DAC for 48 hours, respectively. Dead cells were removed with dead cell removal microbeads and live cells were used for RRBS
|
| Growth protocol |
B16F10 cell line was a kind gift of Gordon Freeman (Dana-Farber Cancer Institute). 4T1 cells were provided by Fred Miller (Wayne State University). Cells were cultured with Dulbecco’s modified Eagle medium (DMEM) supplemented with 10% heat-inactivated fetal bovine serum (FBS, VWR), 6 mM HEPES, 1.6 mM L-glutamine, 50 mM 2-mercaptoethanol, 100 U/ml penicillin G and 100 mg/ml streptomycin sulfate (Sigma-Aldrich). All cell lines were verified to be free of mycoplasma by PCR and were authenticated by morphology.
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
genomic DNA was isolated with Quick-DNA Microprep Kit (ZYMO RESEARCH).
100 ng gDNA was used for library preparation following Zymo-Seq RRBS Library Kit
|
| |
|
| Library strategy |
Bisulfite-Seq |
| Library source |
genomic |
| Library selection |
Reduced Representation |
| Instrument model |
Illumina NovaSeq 6000 |
| |
|
| Data processing |
The raw fastq files were trimmed for the adaptors and filling nucleotides using trim Galore
The Trimed reads were mapped to mouse genome (mm10) and methylation calls were performed using Bismark
Differentially methylated regions (DMR) between DAC-treated and control cell lines were determined using Metilene software package
Significant DMR in 4T1 cell line were determined using FDR<1E-16 cut-off. Significant DMR in B16 cell line were determined using FDR<1E-10 cut-off
Assembly: mm10
Supplementary files format and content: bigWig and bedGraph
|
| |
|
| Submission date |
Aug 25, 2022 |
| Last update date |
Jul 01, 2024 |
| Contact name |
Eric Greer |
| E-mail(s) |
Eric.Greer@childrens.harvard.edu
|
| Organization name |
Boston Children's Hospital/Harvard Medical School
|
| Department |
Newborn Medicine/Department of Pediatrics
|
| Lab |
Greer Lab
|
| Street address |
320 Longwood Avenue
|
| City |
Boston |
| State/province |
MA |
| ZIP/Postal code |
02115 |
| Country |
USA |
| |
|
| Platform ID |
GPL24247 |
| Series (2) |
| GSE212028 |
Genomewide methylation analysis of B16F10 and 4T1 after Decitabine treatment with Reduced Representative Bisulfite Sequencing [RRBS] |
| GSE212029 |
B16 and 4T1 cell lines with decitabine treatment |
|
| Relations |
| BioSample |
SAMN30497040 |
| SRA |
SRX17212159 |
