|
| Status |
Public on Dec 22, 2021 |
| Title |
Female ESC 2 |
| Sample type |
SRA |
| |
|
| Source name |
ES cell line
|
| Organism |
Mus musculus |
| Characteristics |
strain: C57BL6
cell type: Female ES cell line
|
| Treatment protocol |
For the induced PGCLCs, ESCs or pESCs treated with 1%KSR, 1. ng/ml bFGF and 2ng/ml Activin A for 2 days can form EpiLCs, and further treated with 500 ng/ml BMP4, 100 ng/ml SCF, 50ng/ml EGF and 1000 IU mLif for 4 days to form PGCLCs.
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
Cells were collected and isolated their genomic DNA by QIAamp DNA Micro Kit (QIAGEN)
DNA purity was checked using the NanoPhotometer® spectrophotometer (IMPLEN, CA, USA) and DNA concentration was measured using Qubit® DNA Assay Kit in Qubit® 2.0 Flurometer (Life Technologies, CA, USA). A total amount of 1.5 μg DNA spiked with moderate lambda DNA was handled by MspI, followed by end repair and adenylation. Cytosine-methylated barcodes were ligated to sonicated DNA as per manufacturer’s instructions. Then these DNA fragments were treated twice with bisulfite using EZ DNA Methylation-GoldTM Kit (Zymo Research), before the resulting single-strand DNA fragments were PCR amplified using KAPA HiFi HotStart Uracil and ReadyMix (2X). Library concentration was quantified by Qubit® 2.0 Flurometer and quantitative PCR, and the insert size was assayed on Agilent Bioanalyzer 2100 system. The library preparations were sequenced on an Illumina Novaseq platform and 125bp/150bp paired-end reads generated. Image analysis and base calling were performed with Illumina CASAVA pipeline, and finally 125bp/150bp paired-end reads were generated.
|
| |
|
| Library strategy |
Bisulfite-Seq |
| Library source |
genomic |
| Library selection |
Reduced Representation |
| Instrument model |
Illumina NovaSeq 6000 |
| |
|
| Data processing |
Bismark software (version 0.16.3) was used to perform alignments of bisulfite-treated reads to a reference genome.
The reference genome was firstly transformed into bisulfite-converted version (C-to-T and G-to-A converted) and then indexed using bowtie2.
Sequence reads were also transformed into fully bisulfite-converted versions (C-to-T and G-to-A converted) before they are aligned to similarly converted versions of the genome in a directional manner.
Sequence reads that produce a unique best alignment from the two alignment processes (original top and bottom strand) are then compared to the normal genomic sequence and the methylation state of all cytosine positions in the read is inferred.
Genome_build: mm10
|
| |
|
| Submission date |
Jul 07, 2020 |
| Last update date |
Dec 22, 2021 |
| Contact name |
Chenglei Tian |
| E-mail(s) |
chenglei.tian@helmholtz-munich.de
|
| Organization name |
Helmholtz Munich
|
| Lab |
Instirution of translational stem cell research
|
| Street address |
Ingolstädter Landstraße 1
|
| City |
Munich |
| ZIP/Postal code |
85764 |
| Country |
Germany |
| |
|
| Platform ID |
GPL24247 |
| Series (2) |
| GSE153979 |
Amplification of Germ Cells through Parthenogenesis Faithfully Maintain Genomic Imprinting [RRBS] |
| GSE154145 |
Amplification of Germ Cells through Parthenogenesis Faithfully Maintain Genomic Imprinting |
|
| Relations |
| BioSample |
SAMN15468583 |
| SRA |
SRX8683690 |
