|
| Status |
Public on Jan 19, 2023 |
| Title |
SOa1 |
| Sample type |
SRA |
| |
|
| Source name |
mouse blastocyst
|
| Organism |
Mus musculus |
| Characteristics |
tissue: mouse blastocyst
oocyte collection_method: superovulation of adult mouse
treatment: LSC15
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
Blastocysts were individually collected and lysed in 10 μl of RLT buffer
DNA was purified using solid phase reversible immobilization (SPRI) beads and converted with bisulphite reagent using EZ DNA Methylation-Gold kit (ZYMO Research, D5005). DNA was eluted in EB buffer and individual blastocyst PBAT libraries were prepared as outlined below. First-strand synthesis was performed using Klenow exo-tagged (New England Biolabs) and a biotinylated oligo I (5-[Btn]CTACACGACGCTCTTCCGATCTNNNNNNNNN-3), followed by Exo-I treatment (New England Biolabs) and SPRI purification. Purified DNA was incubated with Dynabeads Strepatavidin M-280 beads (ThermoFisher Scientific) to capture biotinylated DNA and second strand synthesis was carried out using reverse oligo II (5’-TGCTGAACCGCTCTTCCGATCTNNNNNNNNN 3’). Libraries were amplified using indexed iPCRTag reverse primers (54) with KAPA HiFi (Kapa Biosystem) DNA polymerase for 15 PCR cycles and purified using SPRI beads (Agencourt Ampure XP bead). Libraries were quantitated and quality control was checked using Agilent High Sensitivity DNA kit and KAPA Illumina Library Quantifcation Kit for Illumina (KAPA Biosystems)
Bisulfite-Seq (PBAT)
|
| |
|
| Library strategy |
Bisulfite-Seq |
| Library source |
genomic |
| Library selection |
RANDOM |
| Instrument model |
Illumina NextSeq 500 |
| |
|
| Data processing |
Fastq files were aligned using Bismark v0.20.1 in PBAT mode against the GRCm38 genome where SNP positions between C57B6 and CBA were N masked using the SNPSplit_genome_preparation script.
Bismark BAM files were split into reads deriving from C57B6, CBA or Undefined BAM files using SNPsplit v0.4
Methylation calls were extracted from the split BAM files using the bismark methylation extractor with default parameters
Assembly: GRCm38
Supplementary files format and content: CpG methylation counts in Bismark coverage file format
|
| |
|
| Submission date |
May 30, 2022 |
| Last update date |
Jan 19, 2023 |
| Contact name |
Simon Richard Andrews |
| E-mail(s) |
simon.andrews@babraham.ac.uk
|
| Phone |
+441223496000
|
| Organization name |
The Babraham Institute
|
| Department |
Science Services
|
| Lab |
Bioinformatics
|
| Street address |
Babraham Research Campus
|
| City |
Cambridge |
| State/province |
Cambs |
| ZIP/Postal code |
CB22 3AT |
| Country |
United Kingdom |
| |
|
| Platform ID |
GPL19057 |
| Series (1) |
| GSE205097 |
Genome-wide assessment of DNA methylation alterations induced by superovulation, sexual immaturity and in vitro follicle growth in mouse blastocysts |
|
| Relations |
| BioSample |
SAMN28767418 |
| SRA |
SRX15499595 |
