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| Status |
Public on Dec 16, 2015 |
| Title |
BisSeq_TKO |
| Sample type |
SRA |
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| Source name |
embryonic stem cells
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| Organism |
Mus musculus |
| Characteristics |
strain: 159 (mixed 129-C57Bl/6)
genotype: DNMT TKO
growth condition: serum
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| Growth protocol |
Mouse embryonic stem cells were cultivated without feeders on 0.2% gelatine-coated dishes in DMEM, supplemented with 15% fetal calf serum, 1× non-essential amino acids, 2 mM L-glutamine, LIF and 0.001% β-mercaptoethanol (37°C, 7% CO2).
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| Extracted molecule |
genomic DNA |
| Extraction protocol |
DNA was isolated by phenol chloroform extraction, followed by ethanol precipitation.
Library Construction Protocol: 5 μg of sonicated genomic DNA were end repaired and 3′-end adenylated using the Illumina TruSeq DNA LT Sample Preparation kit (Illumina 15025064). Paired-end adapters were ligated to the DNA fragments and adaptor-ligated DNA was purified by 2% agarose gel electrophoresis. The gel-purified DNA was converted with the EpiTect Bisulfite kit (Qiagen). Converted libraries were enriched by 10 cycles of PCR using PfuTurbo Cx Hotstart DNA Polymerase (Agilent) and purified using AMPure XP beads. Quality of the libraries and size distribution was assessed on an Agilent 2100 Bioanalyzer (Agilent Technologies). Sequencing was performed on an Illumina HiSeq 2500 machine (100 bp read length, paired end) according to Illumina standards.
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| Library strategy |
Bisulfite-Seq |
| Library source |
genomic |
| Library selection |
RANDOM |
| Instrument model |
Illumina HiSeq 2500 |
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| Data processing |
Basecalling was performed with the Illumina RTA 1.17.21.3 software with default parameters
Fastq files were generated with the Illumina bcl2fastq-1.8.4 software with options --use-bases-mask Y50n,I6n --fastq-cluster-count 100000000 --no-eamss
Bis-seq reads were processed with QuasR and positions covered by at least 10 reads were used.
Genome_build: mm9
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| Submission date |
Sep 23, 2015 |
| Last update date |
May 15, 2019 |
| Contact name |
Anais Flore Bardet |
| Organization name |
IGBMC
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| Street address |
1 rue Laurent Fries
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| City |
Illkirch |
| ZIP/Postal code |
67404 |
| Country |
France |
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| Platform ID |
GPL17021 |
| Series (1) |
| GSE67867 |
Competition between DNA methylation and transcription factors determines binding of NRF1 |
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| Relations |
| BioSample |
SAMN04103868 |
| SRA |
SRX1280454 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSM1891661_BisSeq_TKO.tsv.gz |
59.7 Mb |
(ftp)(http) |
TSV |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data provided as supplementary file |
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