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Sample GSM7712391 Query DataSets for GSM7712391
Status Public on Dec 20, 2023
Title ZFP-ETRs against Pcsk9 treated hepatocytes, replicate 1
Sample type SRA
 
Source name Liver
Organism Mus musculus
Characteristics tissue: Liver
cell type: Hepatocytes
strain: C57BL/6
treatment: ZFP-ETRs against Pcsk9
Extracted molecule genomic DNA
Extraction protocol Genomic DNA extraction by Maxwell® 16 Cell LEV DNA Purification Kit and biisufite conversion by EpiTect Bisulfite Kit, following provider indications. Finally, the promoter region of Arid1b and Shroom1 was amplified by PCR.
Libraries were prepared using NEBNext® Ultra™ II DNA Library Prep Kit for Illumina following the manufacturer’s recommendations
 
Library strategy Bisulfite-Seq
Library source genomic
Library selection RANDOM
Instrument model Illumina MiSeq
 
Data processing Reads quality was controlled with Fastqc v0.11.9 while low-quality reads and adapters were removed using Trim_Galore v0.6.6. with the following parameters: --quality 20, --length 25, --paired, --rrbs
Remaining reads were analyzed using the Bismark read mapper Methylation caller tool v0.23.0
In detail, reads were aligned to both unconverted and converted genomes (GRCm38) using bismark with the --local and –non_directional parameters and the methylation status was obtained using bismark_methylation_extractor script using only the reads mapping to the bottom strand (OB and CTOB)
The methylation calls were processed using the R/Bioconductor package MethylKit v1.16.1
Imported data were filtered to retain only cytosines from CpG context in the amplified windows and normalized using the normalizeCoverage function
The information from the different samples was merged using the unite function considering the positions covered in at least 1 replicate per condition. The methylation percentage at each position was calculated using the percMethylation function.
Assembly: GRCm38
Supplementary files format and content: Bismark coverage
 
Submission date Aug 16, 2023
Last update date Dec 20, 2023
Contact name Sara Valsoni
E-mail(s) [email protected]
Organization name SR-TIGET
Department TIGET
Street address via Olgettina 60
City Milano
State/province MI
ZIP/Postal code 20132
Country Italy
 
Platform ID GPL16417
Series (2)
GSE226209 Durable and efficient gene silencing in vivo by hit-and-run epigenome editing
GSE240935 Durable and efficient gene silencing in vivo by hit-and-run epigenome editing [targetBSseq_offTargets]
Relations
BioSample SAMN37000932
SRA SRX21380873

Supplementary file Size Download File type/resource
GSM7712391_ZFP_ETRs_1_offTargets.bismark.cov.gz 7.7 Kb (ftp)(http) COV
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file

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