|
| Status |
Public on Dec 08, 2020 |
| Title |
Knock Down YAP T0 Rep 2 (BS-Seq) |
| Sample type |
SRA |
| |
|
| Source name |
embryonic stem cells
|
| Organism |
Mus musculus |
| Characteristics |
cell type: embryonic stem cells
cell differentiation: Undifferentiated
developmental stage: pluripotent
treatment: Transient transfection with siRNAs targeting mYAP
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
Genomic DNA from two independent experiment was extracted and purified by QIAamp DNA Kit (QIAGEN) according to the manufacturer’s instructions.
Illumina SureSelectXT Methyl-Seq Target Enrichment System
|
| |
|
| Library strategy |
Bisulfite-Seq |
| Library source |
genomic |
| Library selection |
RANDOM |
| Instrument model |
Illumina NextSeq 500 |
| |
|
| Description |
KD YAP-2 T0
|
| Data processing |
Reads have been quality trimmed using trim galore with parameters --paired --trim1 --phred33 -j 4
Mapping on in silico bisulphitated mm9 genome have been carried out using Bismark/Bowtie2 with parameter -p 12 -X 1000
Methylated positions have been called using the processBismarkAln of methylKit
Differentially methylated regions (DMRs) have been calles using the tileMethylCounts and calculateDiffMeth of functions of methylKit with window size 250bp and step size 125bp.
Genome_build: mm9 (bisulphitated in silico using Bismark)
Supplementary_files_format_and_content: Differential Methylated Regions analysis (tabular file). DMR_analysis.xlsx contains the DMRs between CTRL0/YAP0, CTRL4/YAP4, CTRL0/CTRL4, and YAP0/YAPT4 with the associated qvalue and % of diff.
|
| |
|
| Submission date |
Sep 09, 2020 |
| Last update date |
Dec 08, 2020 |
| Contact name |
Federico Zambelli |
| Organization name |
University of Milan
|
| Department |
Department of Biosciences
|
| Street address |
Via Giovanni Celoria 26
|
| City |
Milano |
| ZIP/Postal code |
20133 |
| Country |
Italy |
| |
|
| Platform ID |
GPL19057 |
| Series (2) |
| GSE157704 |
Methylation pattern profile of mouse embryonic stem cells upon knockdown of YAP, during neuroectodermal differentiation |
| GSE157707 |
YAP contributes to DNA methylation remodeling upon mouse embryonic stem cell differentiation |
|
| Relations |
| BioSample |
SAMN16086833 |
| SRA |
SRX9098954 |
