|
| Status |
Public on Nov 14, 2016 |
| Title |
wt_Mx_pos_825 [Bisulfite-Seq] |
| Sample type |
SRA |
| |
|
| Source name |
bone marrow
|
| Organism |
Mus musculus |
| Characteristics |
cell type: LSK
strain: C57BL/6
genotype: wt_Mx+
|
| Treatment protocol |
Mx1-driven Cre-mediated recombination was induced by 5 IP injections of poly(I:C)
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
bone marrow was extracted from femurs, tibiae and iliac crests. After red blood cell lysis and magnetic lineage depletion cells were FACS-sorted to isolate Lin- Sca1+ cKit+ (LSK) cells. Total RNA was extracted using AllPrep Kit (Qiagen)
Genomic DNA was purified from murine cells, digested with MspI restriction enzyme, subjected to end repair and adenylation followed by ligation to cytosine methylated paired-end Illumina adaptors. Fragments of 150-400 bp were isolated by size selection and subjected to bisulfite conversion and PCR amplification using paired-end Illumina primers. Libraries were sequenced using an Illumina HiSeq2500 per manufacturer’s recommended protocol for 50bp single end read reads
|
| |
|
| Library strategy |
Bisulfite-Seq |
| Library source |
genomic |
| Library selection |
RANDOM |
| Instrument model |
Illumina HiSeq 2500 |
| |
|
| Data processing |
Illumina Casava1.8 software used for basecalling.
Sequenced reads were trimmed for adaptor sequences and then mapped to mm10 using a whole genome bismark alignment software approach with a maximum of 2 mismatches in a directional manner allowed. Only uniquely aligned reads were retained. Reads which pass filter were considered for mapping. If both matched reads pass filter, the last base of R2 was compared to the first base of R1 (one base overlap); the base with the best quality score was retained and R1 was concatenated to R2 for use in alignment.
methylation score were determined for cytosines with at least 20 phred quality score and 10× coverage
Percentage of bisulfite converted Cytosines (Cs; representing unmethylated Cs) and non-converted Cs (representing methylated Cs) were recorded for each C position in a CpG context
Percent methylation values for CpG dinucleotides are calculated by dividing the number of methylated Cs by total coverage on that base (Cs and Ts).
Genome_build: mm10, ENSEMBL Mus_musculus.GRCm38.75
Supplementary_files_format_and_content: tab-delimited text files include the number of methylated Cs and Ts per position (base) covered
|
| |
|
| Submission date |
Sep 12, 2016 |
| Last update date |
May 15, 2019 |
| Contact name |
Barbara Spitzer |
| E-mail(s) |
spitzerb@mskcc.org
|
| Organization name |
Memorial Sloan Kettering Cancer Center
|
| Lab |
Levine Lab
|
| Street address |
411 E 67th St
|
| City |
New York |
| State/province |
NY |
| ZIP/Postal code |
10065 |
| Country |
USA |
| |
|
| Platform ID |
GPL17021 |
| Series (2) |
| GSE72883 |
DNMT3A R882 mutations promote anthacyline resistance through impaired DNA-damage sensing |
| GSE86827 |
DNMT3A R882 mutations promote anthacyline resistance through impaired DNA-damage sensing [Bisulfite-Seq] |
|
| Relations |
| BioSample |
SAMN05763060 |
| SRA |
SRX2159798 |
