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Sample GSM1517800 Query DataSets for GSM1517800
Status Public on May 19, 2016
Title WT3a_FLT3_RRBS_2 RRBS
Sample type SRA
 
Source name Bone marrow
Organism Mus musculus
Characteristics tissue: bone marrow
cell type: Leukemic cells
genotype: Mx1-cre+;Dnmt3a+/+;MSCV_FLT3-ITD-GFP
strain: C57BL/6
Treatment protocol Adapter-ligated fragments were bisulfite converted with Qiagen Epitect kit.
Growth protocol Bulk or Sca1+ enriched Dnmt3a KO or WT murine bone marrow cells were transduced with retroviruses expressing MSCV-FLT3-ITD-IRES-GFP or MSCV-GFP transgenes and transplanted into lethally irradiated recipients by retro-orbital injections. Whole bone marrow cells from each genotype were collected from transplant recipients.
Extracted molecule genomic DNA
Extraction protocol Extract DNA using Qiagen Allprep Mini kit.
Tru-Seq DNA sample prep kit
 
Library strategy Bisulfite-Seq
Library source genomic
Library selection Reduced Representation
Instrument model Illumina HiSeq 2000
 
Description Biological replicate 2 of FLT3-ITD leukemia RRBS. Donor whole bone marrow cells were subjected to to retroviral transduction and transplantation
Data processing Base quality- and adapter-trimmed Fastq files were aligned with bsmap 2.73 in RRBS mode using the following parameters: -g 1 -w 5 -D C-CGG -p 8 -R -s 12 -S 42 -u; methylation ratios were calculated with the bsmap utility script methratio.py using the following parameters: -z --ct-snp=no-action
Genome_build: mm9
Supplementary_files_format_and_content: text output of bsmap utility methratio.py; chromosome, coordinate (1-based), strand, sequence context (2nt upstream to 2nt downstream in Watson strand direction), methylation ratio, number of effective total C+T counts on this locus, number of total C counts on this locus, number of total C+T counts on this locus, number of total G counts on this locus of reverse strand, number of total G+A counts on this locus of reverse strand, lower bound of 95% confidence interval of methylation ratio, calculated by Wilson score interval for binomial proportion, upper bound of 95% confidence interval
 
Submission date Oct 01, 2014
Last update date May 15, 2019
Contact name Margaret Goodell
Organization name Baylor College of Medicine
Street address One Baylor Plaza, N1030
City Houston
State/province TX
ZIP/Postal code 77030
Country USA
 
Platform ID GPL13112
Series (2)
GSE61970 RRBS assessment of global methylation alterations alterations in Dnmt3aKO/FLT3-ITD leukemia
GSE61971 Molecular profiling of mouse Dnmt3a/FLT3-ITD leukemia models
Relations
BioSample SAMN03085880
SRA SRX718855

Supplementary file Size Download File type/resource
GSM1517800_GJ32805.RRBS.newmeth.txt.gz 70.2 Mb (ftp)(http) TXT
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file

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