|
| Status |
Public on Feb 03, 2024 |
| Title |
WGBS iPSC TF15 |
| Sample type |
SRA |
| |
|
| Source name |
induced pluripotent stem cells
|
| Organism |
Mus musculus |
| Characteristics |
cell type: induced pluripotent stem cells
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
Cells were lysed in cell lysis buffer with Proteinase K solution and then genomic DNA was extracted from cells using the phenol:chloroform extraction method. Genomic DNA was then purified using Zymo Genomic DNA Clean & Concentrator kit according to the manufacturer’s instructions.
About 50ng of genomic DNA from each sample was subjected to bisulfite conversion. Preparation of the WGBS libraries was done using the Zymo Pico Methyl-Seq Library Prep Kit according to the manufacturer’s instructions.
|
| |
|
| Library strategy |
Bisulfite-Seq |
| Library source |
genomic |
| Library selection |
RANDOM |
| Instrument model |
Illumina HiSeq 3000 |
| |
|
| Data processing |
WGBS data were processed using the comprehensive wg-blimp v10.0.0 software pipeline. In brief, all reads were trimmed with Trim Galore v0.6.5 to remove adaptors and the first four bases. Reads were mapped onto the mouse reference genome GRCm39 using bwa-meth and PCR duplicates were removed with the Picard toolkit. The analysis of differentially methylated regions (DMRs) was performed using metilene and BSmooth algorithms. Hierarchical clustering was performed using the clusterSamples function and PCA was performed using the PCASamples function from methylKit v1.22.0 using the percent methylation matrix as an input
Assembly: GRCm39
Supplementary files format and content: bedGraph
|
| |
|
| Submission date |
Jan 29, 2024 |
| Last update date |
Feb 03, 2024 |
| Contact name |
Yu-Huey Lin |
| E-mail(s) |
[email protected]
|
| Organization name |
The University of Texas at San Antonio
|
| Department |
The Department of Neuroscience, Developmental and Regenerative Biology
|
| Street address |
One UTSA Circle,
|
| City |
San Antonio |
| State/province |
Texas |
| ZIP/Postal code |
78249 |
| Country |
USA |
| |
|
| Platform ID |
GPL21493 |
| Series (2) |
| GSE254456 |
Source cell-type epigenetic memory persists in induced pluripotent cells but is lost in subsequently derived germline cells [WGBS] |
| GSE254465 |
Source cell-type epigenetic memory persists in induced pluripotent cells but is lost in subsequently derived germline cells |
|
| Relations |
| BioSample |
SAMN38334538 |
| SRA |
SRX22585380 |
