|
| Status |
Public on Oct 20, 2014 |
| Title |
NCCIT siDNMT3B 5mC-seq |
| Sample type |
SRA |
| |
|
| Source name |
NCCIT human cells depleted of DNMT3B by siRNA
|
| Organism |
Homo sapiens |
| Characteristics |
cell line: NCCIT
cell type: embryonic carcinoma cells
transfected with: siRNA against DNMT3B
affinity purification method: MethylMagnet mCpG DNA isolation (Ribomed)
|
| Treatment protocol |
NCCIT cells were transfected with siRNA (Dharmacon) against DNMT3B, and a no-target control (NTC)
|
| Growth protocol |
NCCIT cells were cultured in McCoy’s 5A medium (Invitrogen) supplemented with 2 mm L-glutamine (Mediatech) and 10% heat-inactivated fetal bovine serum (Hyclone).
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
Genomic DNA was isolated by proteinase digestion and phenol:chloroform extraction. Affinity purification was performed according to manufacturers' protocols.
DNA sequencing libraries were constructed according to Illumina's protocol for TruSeq DNA sample preparation kit
|
| |
|
| Library strategy |
MBD-Seq |
| Library source |
genomic |
| Library selection |
MBD2 protein methyl-CpG binding domain |
| Instrument model |
Illumina HiSeq 2000 |
| |
|
| Description |
Sample 2
|
| Data processing |
Basecalls performed using CASAVA version 1.7
MBD-seq reads were aligned to the hg19 genome assembly using BWA version 0.5.9.
Mapped reads were filtered if they were mapped to multiple locations and to unique location with 5% or more mismatches and indels of read lengths.
peaks were called using SICER version 1.1 with the following setting: Window Size (200),Gap Size (400), Effective genome size (0.854).
differential peaks were called using SICER version 1.1 with the following setting: Window Size (200),Gap Size (400).
Genome_build: hg19
Supplementary_files_format_and_content: bed.gz files were generated using bamToBed and gzip
Supplementary_files_format_and_content: bigwig files were generated using wigToBigWig; Scores represent read depth.
|
| |
|
| Submission date |
Feb 10, 2014 |
| Last update date |
May 15, 2019 |
| Contact name |
Keith D Robertson |
| E-mail(s) |
robertson.keith@mayo.edu
|
| Phone |
507-266-4886
|
| Organization name |
Mayo Clinic
|
| Department |
Molecular Pharmacology & Experimental Therapeutics
|
| Lab |
Epigenetic Etiology of Human Disease Laboratory
|
| Street address |
200 First Street SW, Stabile 12-70
|
| City |
Rochester |
| State/province |
MN |
| ZIP/Postal code |
55905 |
| Country |
USA |
| |
|
| Platform ID |
GPL11154 |
| Series (2) |
| GSE54842 |
Acute depletion redefines the division of labor among DNA methyltransferases in methylating the human genome [MBD-seq] |
| GSE54843 |
Acute depletion redefines the division of labor among DNA methyltransferases in methylating the human genome |
|
| Relations |
| BioSample |
SAMN02639654 |
| SRA |
SRX469036 |
