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Sample GSM5517036 Query DataSets for GSM5517036
Status Public on Dec 04, 2023
Title WT_SPL_HSC_2 [bisulfite-seq]
Sample type SRA
 
Source name Spleen
Organism Mus musculus
Characteristics strain: C57BL/6
genotype: WT
cell type: Splenic hematopoietic stem cells
treatment: PHZ
Treatment protocol 60mg/kg of phenylhydrazine (PHZ) was injected intraperitoneally for two constitutive days. Cells were sorted at day 3 after the last injection.
Growth protocol Mice were housed in AAALAC-accredited, specific-pathogen-free animal care facilities at Baylor College of Medicine (BCM) with 12-hour light-dark cycle and received standard chow ad libitum. All procedures were approved by the BCM (protocol #AN-5858) Institutional Animal Care and Use Committees.
Extracted molecule genomic DNA
Extraction protocol Genomic DNA was purified from sorted HSCs followed by bisulfite conversion and bisulfite PCR to amplify the region of interest (Tfrc gene).
The PCR products were purified and prepped for amplicon-seq using the Illumina Nextera XT kit.
 
Library strategy Bisulfite-Seq
Library source genomic
Library selection RANDOM
Instrument model Illumina NextSeq 500
 
Data processing The reads were aligned with bsmapz.
Methylation calculations were done using MethPipe.
Genome_build: mm10
Supplementary_files_format_and_content: tab-delimited text files include methylation measurements from MethPipe
 
Submission date Aug 13, 2021
Last update date Dec 04, 2023
Contact name Rebecca Murdaugh
Organization name Baylor College of Medicine
Street address One Baylor Plaza
City Houston
State/province Texas
ZIP/Postal code 77030
Country USA
 
Platform ID GPL19057
Series (2)
GSE182058 The effect of PHZ-induced hemolytic anemia on HSCs [bisulfite-seq]
GSE182059 The effect of PHZ-induced hemolytic anemia on HSCs
Relations
BioSample SAMN20770761
SRA SRX11742521

Supplementary file Size Download File type/resource
GSM5517036_S5_Tfrc_CpG.meth.txt.gz 182 b (ftp)(http) TXT
GSM5517036_S5_Tfrc_CpG.sym.meth.txt.gz 142 b (ftp)(http) TXT
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file

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