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GEO help: Mouse over screen elements for information. |
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| Status |
Public on Jun 27, 2013 |
| Title |
Serum P12 (3) BS-Seq |
| Sample type |
SRA |
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| Source name |
ES cells
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| Organism |
Mus musculus |
| Characteristics |
cell line: E14 ES
passages: 12
strain: 129P2/Ola
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| 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)).
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| 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.
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| Library strategy |
Bisulfite-Seq |
| Library source |
genomic |
| Library selection |
RANDOM |
| Instrument model |
Illumina HiSeq 1000 |
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| 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
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| Submission date |
Dec 14, 2012 |
| Last update date |
May 15, 2019 |
| Contact name |
Felix Krueger |
| E-mail(s) |
fkrueger@altoslabs.com
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| Organization name |
Altos Labs
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| Department |
Bioinformatics
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| Street address |
Granta Park
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| City |
Cambridge |
| ZIP/Postal code |
CB21 6GP |
| Country |
United Kingdom |
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| Platform ID |
GPL15103 |
| Series (1) |
| GSE42923 |
FGF Signaling Inhibition in ESCs Drives Rapid Genome-wide Demethylation to the Epigenetic Ground State of Pluripotency |
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| Relations |
| SRA |
SRX210601 |
| BioSample |
SAMN01831320 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSM1053459_E14_ES_Serum_P12_3_CpG_methylation_calls.txt.gz |
781.3 Mb |
(ftp)(http) |
TXT |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data provided as supplementary file |
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