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GEO help: Mouse over screen elements for information. |
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| Status |
Public on Jul 20, 2022 |
| Title |
HA36_WT_ES |
| Sample type |
SRA |
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| Source name |
Mouse Embryonic Stem Cells
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| Organism |
Mus musculus |
| Characteristics |
cell type: embryonic stem cells
genotype: wild type
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| Growth protocol |
ES cells were were cultivated on feeder cells or 0.2% gelatine coated dishes. ES cell growth medium consisted of DMEM (Invitrogen) supplemented with 15% foetal calf serum (Invitrogen), 1x non-essential amino acids (Invitrogen), 1mM L-glutamine, LIF and 0.001% beta-mercaptoethanol.
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| Extracted molecule |
genomic DNA |
| Extraction protocol |
Genomic DNA extraction, followed by phenol/chloroform extraction and ethanol precipitation. RNaseA treatment was performed for 30 min at 37C
Gemomic DNA was converted using the Qiagen Epitect bisulphite conversion kit. After conversion, two separate PCR amplifications per target were performed at 50 ˚C and 58 ˚C annealing temperature with the PhusionU polymerase (Thermo Scientific) for 45 cycles of 1 min 95 ˚C denaturation, 1 min for annealing, and 1 min 72 ˚C for extension. PCR products were run on a 1.2 % agarose gel, extracted, quantified and pooled at equimolar ratios. Library preparation was done with 10 ng of input material using the NEBNext Ultra II kit protocol and cleaned up using Ampure XP beads (Beckman Coulter).
targeted bisuphite PCR- seq
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| Library strategy |
Bisulfite-Seq |
| Library source |
genomic |
| Library selection |
RANDOM |
| Instrument model |
Illumina NovaSeq 6000 |
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| Description |
bsPCR-amplicons
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| Data processing |
Sequencing reads were pre-processed and trimmed using trim_galore v0.6.6 with --paired --clip_R1 10 --clip_R2 10 --nextseq 20
Trimmed reads were mapped against the mm10 mouse assembly using Bismark v0.23.0 bismark with --non_directional
methylation calling was done with Bismark v0.23.0 bismark_methylation_extractor with --bedgraph
Genome_build: mm10
Supplementary_files_format_and_content: Processed tab delimited file contains bismark coverage report with following information: chromosome, start, end, average methylation, reported methylated cytosines, reported unmethylated cytosines
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| Submission date |
Jun 09, 2021 |
| Last update date |
Jul 20, 2022 |
| Contact name |
Tuncay Baubec |
| Organization name |
Utrecht University
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| Department |
Department of Biology
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| Lab |
Genome Biology and Epigenetics
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| Street address |
Padualaan 8
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| City |
Utrecht |
| ZIP/Postal code |
3584 CH |
| Country |
Netherlands |
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| Platform ID |
GPL24247 |
| Series (2) |
| GSE176460 |
DNA sequence determines epigenetic bistability at imprinting control regions [BS-Seq] |
| GSE176461 |
DNA sequence and chromatin modifiers determine epigenetic bistability at imprinting control regions |
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| Relations |
| BioSample |
SAMN19642209 |
| SRA |
SRX11099940 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSM5365934_20210427.B-o24674_1_15-SB_bsMIX_007_R1_val_1_bismark_bt2_pe.bismark.cov.gz |
11.7 Kb |
(ftp)(http) |
COV |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data provided as supplementary file |
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