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Sample GSM4577402 Query DataSets for GSM4577402
Status Public on Dec 07, 2020
Title H-IGF2
Sample type SRA
 
Source name Peritoneal macrophages
Organism Mus musculus
Characteristics strain: C57BL/6
Sex: Female
treatment: 1,000 ng IGF2 treated twice
Treatment protocol Peritonitis was induced by i.p. injection of 2 ml of 4% (weight/volume) thioglycollate broth media (Ftg, BD). After 24 h and 48 h, mice were injected with IGF2 (R&D Systems) at either low doses (5 ng per mouse; L-IGF2) or a high dose (1,000 ng per mouse, H-IGF2). Peritoneal cells were harvested on day 3.
Extracted molecule genomic DNA
Extraction protocol Total DNA was isolated using the QIAamp DNA Mini Kit (Qiagen).
A bisulfite library was prepared according to the Illumina protocol essentially as described (Rademacher et al., 2014). The 667 million read pairs were cleared by the NGSQC toolkit (Dai et al., 2010), excluding reads with a mapping quality lower than 30 (probability to map at a correct position = 0.999) and ignoring bases with base quality lower than 20 (probability that the sequencing process produced the correct base = 0.99). Finally, above 90 gigabytes data of each sample were executed by the bismark tool and a modified Mus musculus reference (GRCm38.p6) to output discriminates between cytosine in the CpG, CHG and CHH context (Krueger and Andrews, 2011).
 
Library strategy Bisulfite-Seq
Library source genomic
Library selection RANDOM
Instrument model HiSeq X Ten
 
Data processing Read pairs were cleared by the NGSQC toolkit to output fastq files
Data were executed by the bismark tool and a modified Mus musculus reference (GRCm38.p6) to output discriminates between cytosine
Discriminates between cytosine in the CpG, CHG and CHH context were revealed in bedgraph files
Genome_build: Mus musculus reference (GRCm38.p6)
Supplementary_files_format_and_content: fastq files were cleared by the NGSQC toolkit
Supplementary_files_format_and_content: bam files were outputed by bismark tool
Supplementary_files_format_and_content: bedgraph files were outputed by bedtools
 
Submission date May 28, 2020
Last update date Dec 07, 2020
Contact name Xuefeng Wang
E-mail(s) wangxuefeng@sibs.ac.cn
Organization name Chinese Academy of Sciences
Street address 320 Yueyang Road
City Shanghai
ZIP/Postal code 200031
Country China
 
Platform ID GPL21273
Series (1)
GSE151404 IGF2R-initiated Proton Rechanneling Dictates an Anti-inflammatory Property in Macrophages
Relations
BioSample SAMN15049239
SRA SRX8419458

Supplementary file Size Download File type/resource
GSM4577402_sample_0_2.mCHH.bedgraph.gz 5.2 Kb (ftp)(http) BEDGRAPH
GSM4577402_sample_1000_4.mCHH.bedgraph.gz 4.1 Kb (ftp)(http) BEDGRAPH
GSM4577402_sample_5_1.mCHH.bedgraph.gz 4.4 Kb (ftp)(http) BEDGRAPH
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file

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