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Status |
Public on Dec 07, 2020 |
Title |
H-IGF2 |
Sample type |
SRA |
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Source name |
Peritoneal macrophages
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Organism |
Mus musculus |
Characteristics |
strain: C57BL/6 Sex: Female treatment: 1,000 ng IGF2 treated twice
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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.
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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).
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Library strategy |
Bisulfite-Seq |
Library source |
genomic |
Library selection |
RANDOM |
Instrument model |
HiSeq X Ten |
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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
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Submission date |
May 28, 2020 |
Last update date |
Dec 07, 2020 |
Contact name |
Xuefeng Wang |
E-mail(s) |
wangxuefeng@sibs.ac.cn
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Organization name |
Chinese Academy of Sciences
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Street address |
320 Yueyang Road
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City |
Shanghai |
ZIP/Postal code |
200031 |
Country |
China |
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Platform ID |
GPL21273 |
Series (1) |
GSE151404 |
IGF2R-initiated Proton Rechanneling Dictates an Anti-inflammatory Property in Macrophages |
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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 Selector |
Raw data are available in SRA |
Processed data provided as supplementary file |
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