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Sample GSM1543542 Query DataSets for GSM1543542
Status Public on Nov 12, 2016
Title Meth_Clone_4T1-Parental_Round_2
Sample type SRA
 
Source name 4T1 Mammary Cancer Cell Line
Organism Mus musculus
Characteristics cell line: Parental Cell Line
Growth protocol DMEM high glucose (Life Technologies) supplemented with 5% fetal bovine serum (Thermo Scientific), 5% fetal calf serum (Thermo Scientific), non-essential amino acids (Life Technologies) and penicillin streptomycin (Life Technologies)
Extracted molecule genomic DNA
Extraction protocol Genomic DNA was purified using the QIAamp DNA Blood Mini Kit (Qiagen) and was fragmented using the Covaris LE220 sonicator according to the manufacturer’s instruction to yield a target fragment size of 300 bp.
The fragmented DNA was end repaired, A-tailored and ligated to methylated Illumina adapters. Ligated fragments were then bisulfite converted using the EZ-DNA Methylation-Gold Kit (Zymo).
Following PCR enrichment, each sample was sequenced on the Illumina HiSeq sequencer generating 76 nt paired-end (PE) reads.
 
Library strategy Bisulfite-Seq
Library source genomic
Library selection RANDOM
Instrument model Illumina HiSeq 2500
 
Description Bisulphate Converted genomic DNA
Data processing 1) Data was processed with Methpipe pipeline to calculate the methylation levels at each CpG and to call hypomethylated regions (Song, Q. et al. A reference methylome database and analysis pipeline to facilitate integrative and comparative epigenomics. PloS one 8, e81148, doi:10.1371/journal.pone.0081148 (2013)).
2) For clustering, the hypomethylated regions of different clones were collapsed together into a consensus set using the Bedtools intersectBed function (merging when a single base of overlap existed).
3) Reads were normalized across samples using DESeq (bioconductor)
4) For each clone, the average methylation levels of the CpGs within the consensus regions were calculated. The median absolute deviations (MAD) of the resultant methylation levels were then used to identify the top 10% most variable for clustering.
5) Promoter methylation levels were calculated as the average CpG methylation level within 1kbp of the transcription start site of each gene. The top 10% most variable promoter regions (based on MAD) were clustered.
Genome_build: mm10
Supplementary_files_format_and_content: HMR_Methylation.txt: field 1 is the chromosome location of the HMR, field 2 is the start position of the HMR, field 3 is the end position of the HMR. All other fields represent the average methylation levels of the different clones within the HMR region. Clones are annotated in the header.
Supplementary_files_format_and_content: Promoter_Methylation.txt: field 1 is the RefSeq gene symbol of the promoter. All other fields represent the average methylation levels of the different clones within the gene promoter region. Clones are annotated in the header.
 
Submission date Nov 11, 2014
Last update date May 15, 2019
Contact name Simon Robert Vincent Knott
Organization name Cold Spring Harbor Laboratory
Department Biology
Lab Hannon
Street address 1 Bungtown Rd
City Cold Spring Harbor
State/province NY
ZIP/Postal code 11724
Country USA
 
Platform ID GPL17021
Series (1)
GSE63181 DNA methylation status of Individual 4T1 Clonal Populations
Relations
BioSample SAMN03175116
SRA SRX757480

Supplementary data files not provided
SRA Run SelectorHelp
Raw data are available in SRA
Processed data are available on Series record

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