 |
 |
GEO help: Mouse over screen elements for information. |
|
| Status |
Public on Sep 30, 2011 |
| Title |
m12_r2 |
| Sample type |
SRA |
| |
|
| Source name |
m12_r2
|
| Organism |
Mus musculus |
| Characteristics |
strain: C57Bl/6
tissue type: Hematopoietic stem cell (HSC)
genotype/variation: wild type (Mx1-cre-;Dnmt3afl/fl)
gender: mixed donor HSC genders
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
50-100ng of genomic DNA digested with 10 Unit MspI (NEB, Ipswich, MA, USA) which cuts at CCGG sites methylation insensitively. Digested fragments were end-repaired, A-tailed and ligated to illumine adapters. End-repair and 3’ adenylation was performed in 50 μl reaction containing 4 mM 5′ methylated dCTP, 4 mM dGTP, 40 mM dATP, and 10U of 3′ to 5′ exo- Klenow DNA polymerase (NEB) and incubated at 30°C for 20 min followed by 20 min at 37°C. Adaptor ligation was performed in 50 μl reactions containing 300mM pre-methylated adapters and 1000 Unit T4 DNA polymerase and incubated at 16 °C overnight. Adaptor-ligated DNA was subjected to a size selection on a 3% NuSieve 3:1 agarose gel. DNA marker lanes were excised from the gel and stained with SYBR Gold (Invitrogen). 160-350 bp slices were excised from the unstained gel and purified using MinElute spin column (Qiagen, Valencia, CA, USA). Size-selected fragments were bisulphite-treated using the EpiTect Bisulphite Kit (Qiagen) with minor modifications by adding 5 more cycles (5 min 95 °C followed by 90 min at 60 °C). After bisulphite conversion, DNA was eluted in 40μl EB buffer and 0.8 μl DNA was used for analytical PCR reactions to determine the minimum number of PCR cycles required to obtain enough material for sequencing. Final PCR products were purified on MinElute columns (Qiagen) and assessed on 4–20% polyacrylamide Criterion TBE Gel (Bio-Rad, Hercules, CA, USA) and quantified using a Qubit fluorometer (Invitrogen).
|
| |
|
| Library strategy |
Bisulfite-Seq |
| Library source |
genomic |
| Library selection |
Reduced Representation |
| Instrument model |
Illumina Genome Analyzer II |
| |
|
| Description |
m12_r2
secondary-transplanted HSCs
Mspi cut fragment at size 40~200bp.
|
| Data processing |
Reads are mapped to genome (mm9) using RRBSMAP, then using a customized pipeline for downstream analysis.
|
| |
|
| Submission date |
Feb 15, 2011 |
| Last update date |
May 15, 2019 |
| Contact name |
deqiang sun |
| E-mail(s) |
dsun@tamu.edu
|
| Phone |
(713) 677-7439
|
| Organization name |
Texas A&M University
|
| Street address |
2121 W Holcombe Blvd
|
| City |
Houston |
| State/province |
TX |
| ZIP/Postal code |
77030 |
| Country |
USA |
| |
|
| Platform ID |
GPL9250 |
| Series (1) |
| GSE27322 |
de novo DNA Methylation Balances Hematopoietic Stem Cell Self-Renewal and Differentiation |
|
| Relations |
| SRA |
SRX043482 |
| BioSample |
SAMN00215970 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSM675440_RRBS_cpgMethylation_m12_r2.bed.gz |
11.7 Mb |
(ftp)(http) |
BED |
| GSM675440_RRBS_rrbsmap_m12_r2.bam |
932.8 Mb |
(ftp)(http) |
BAM |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data provided as supplementary file |
|
|
|
|
 |
