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Sample GSM2373806 Query DataSets for GSM2373806
Status Public on May 29, 2018
Title intermediate-term hematopoietic stem cell rep 1
Sample type SRA
 
Source name Hematopoietic stem cells
Organism Mus musculus
Characteristics strain: C57BL/6
age: 8-12 weeks old
cell type: intermediate-term hematopoietic stem cell
Extracted molecule genomic DNA
Extraction protocol Genomic DNA was isolated from sorted HSPCs using the QIAamp DNA blood mini kit (QIAGEN).
Libraries were constructed using the Pico Methyl-Seq™ library prep kit (Zymo Research), and each library was subjected to 50 bp single-end sequencing on a single lane of a HiSeq 2500 device (Illumina).
 
Library strategy Bisulfite-Seq
Library source genomic
Library selection RANDOM
Instrument model Illumina HiSeq 2500
 
Description cd49bhi_1
Data processing Base-calling and bcl to fastq generation was done with CASAVA 1.8.2 from illumina.
Reads were trimmed with trim_galore (0.4.0) with default options. Adapter sequence AGATCGGAAGAGC was trimmed.
Ran bismark (0.14.3) with option --non_directional. Ran bismark methylation extractor with --report --ignore 10 --ignore_3prime 1 --bedGraph --counts --buffer_size 10G --cytosine_report.
Used R (3.2.2) with bsseq package (1.6.0) to smooth methylation data and find differentially methylated regions.
bigWig tracks were generated in R 3.2.2 by dividing by the total number of alignments and multiplying by 1e6 (rpm).
Genome_build: mm10
Supplementary_files_format_and_content: bigWig tracks with rpm-normalized coverages.
 
Submission date Nov 03, 2016
Last update date May 15, 2019
Contact name Madelaine Gogol
Organization name Stowers Institute
Department Computational Biology Core
Street address 1000 E. 50th Street
City Kansas City
State/province MO
ZIP/Postal code 64110
Country USA
 
Platform ID GPL17021
Series (2)
GSE89490 WGBS assessment of global methylation alterations in hematopoietic stem and progenitor cells [methyl-seq]
GSE89492 A retinoid-dependent and methylation-sensitive enhancer in Hoxb cluster maintains haematopoietic stem cells and prevents leukaemogenesis
Relations
BioSample SAMN05972099
SRA SRX2323931

Supplementary file Size Download File type/resource
GSM2373806_cd49bhi_1.bw 220.3 Mb (ftp)(http) BW
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file

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