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Sample GSM1053456 Query DataSets for GSM1053456
Status Public on Jun 27, 2013
Title P0 BS-Seq
Sample type SRA
 
Source name ES cells
Organism Mus musculus
Characteristics cell line: E14 ES
passages: 0
strain: 129P2/Ola
Growth protocol ESCs were cultured without feeders either in standard serum-containing media (DMEM 4500 mg/L glucose, 4 mM L-glutamine and 110 mg/L sodium pyruvate, 15% fetal bovine serum, 1 U/ml penicillin, 1 μg/ml streptomycin, 0.1mM nonessential amino acids, 50 uM beta-mercaptoethanol, 103 U/ml LIF ESGRO) or under 2i culturing conditions (serum-free N2B27 supplemented with 1000 U/ml LIF and Mek inhibitor PD0325901 (1 uM) and Gsk3 inhibitor CH99021 (3 uM)).
Extracted molecule genomic DNA
Extraction protocol Genomic DNA was prepared using QIAamp DNA Micro Kit or AllPrep DNA/RNA mini kit (QIAGEN). RNA was extracted using either the AllPrep DNA/RNA mini kit or RNeasy® mini kit (QIAGEN) and subjected to DNAase treatment using the Ambion DNA-free™ kit according to the manufacturers’ instructions.
mRNA library preparation for RNA-seq was done as previously described (Ficz et al., 2011). For BS-seq library preparation DNA samples were fragmented by sonication (Covaris) and adaptor ligated (using Illumina supplied methylated adaptors and NEBnext library preparation kit). Subsequently, DNA was bisulfite-treated using the Sigma Imprint kit, according to the manufacturer’s instructions (one step protocol). Final library amplification (16 cycles) was done using Pfu Turbo Cx (Agilent), after which the libraries were gel-purified using QIAGEN Minelute kit.
 
Library strategy Bisulfite-Seq
Library source genomic
Library selection RANDOM
Instrument model Illumina HiSeq 1000
 
Data processing Libraries were sequenced on either an Illumina GAIIx or an Illumina HiSeq using the default RTA (v1.9) analysis software.
Raw Bisulfite-Seq reads were trimmed to remove both poor quality calls and adapters using Trim Galore (v0.2.2, default parameters; www.bioinformatics.babraham.ac.uk/projects/trim_galore/)
Remaining Bisulfite-Seq reads were mapped to the mouse genome (NCBIM37) using Bismark (v0.7.4, default parameters), and CpG methylation calls were extracted using the Bismark methylation extractor (v0.7.4).
RNA-Seq data was mapped to the mouse genome (NCBIM37) assembly using TopHat (v1.4.1, options -g 1) in conjunction with gene models from Ensembl release 61.
Reads were mapped to overlapping transcripts using SeqMonk (www.bioinformatics.babraham.ac.uk/projects/seqmonk/) and log2 read counts per million reads were calculated for all transcripts. Counts were adjusted by matching distributions between samples.
Genome_build: NCBI37
Supplementary_files_format_and_content: Bismark CpG methylation call files are tab delimited and contain 5 colums: (1) read ID; (2) methylation state, whereby '+' = methylated, and '-' = unmethylated; (3) chromosome; (4) position; (5) context call, whereby 'Z' = methylated CpG, and 'z' = unmethylated CpG
Supplementary_files_format_and_content: Quantitated RNA-Seq data files are delimted and contain the following 7 columns: (1) mRNA name (Ensembl); (2) Chromosome; (3) Start; (4) End; (5) Strand; (6) Description (Ensembl); (7) log2 Expression Value
 
Submission date Dec 14, 2012
Last update date May 15, 2019
Contact name Felix Krueger
E-mail(s) fkrueger@altoslabs.com
Organization name Altos Labs
Department Bioinformatics
Street address Granta Park
City Cambridge
ZIP/Postal code CB21 6GP
Country United Kingdom
 
Platform ID GPL15103
Series (1)
GSE42923 FGF Signaling Inhibition in ESCs Drives Rapid Genome-wide Demethylation to the Epigenetic Ground State of Pluripotency
Relations
Reanalyzed by GSE77019
SRA SRX210598
BioSample SAMN01831317

Supplementary file Size Download File type/resource
GSM1053456_E14_ES_P0_CpG_methylation_calls.txt.gz 811.1 Mb (ftp)(http) TXT
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file

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